2965 results for "愛の戦士完全破壊2-re-imagination-version-鞭首絞め・電撃・ヘソか"

in 34.93 milliseconds.

• WGS data of pediatric TCF3::PBX1 acute lymphoblastic leukemia (set1)

  The dataset includes FASTQ and BAM files from diagnostic and matched remission (control) samples of one TCF3::PBX1 ALL patient (ALLT-335). Sequencing library was made using standard PCR-based WGS library preparation (PCR+), using NEB Next® Ultra™ DNA Library Prep Kit. Both diagnostic (90x) and remission (30x) samples were sequenced using HiSeq X.

  Dataset EGAD50000001796

• Plasma cfDNA dataset from healthy donors and cancer patients

  The dataset contains 424 paired-end raw fastq files of 224 plasma cfDNA samples from healthy donors and cancer (Ewing Sarcoma, CIC) patients. WGS and methylation binding domain sequencing was performed at 2 × 150 bp on an NovaSeq6000 or NextSeq 500. 200 samples underwent both WGS and methylation binding domain sequencing. 24 samples underwent only WGS.

  Dataset EGAD50000002051

• WGS data of paediatric BCR::ABL1 acute lymphoblastic leukemia

  The dataset includes FASTQ and CRAM files from diagnostic and matched remission (control) samples of one BCR::ABL1 ALL patient (ALLT-399). Sequencing library was made using PCR free-based WGS library preparation (PCR-), using Novogene NGS DNA Library Prep Set Kit (Cat No. PT004). Both diagnostic (90x) and remission (30x) samples were sequenced using NovaSeqX Plus.

  Dataset EGAD50000002185

• Paired-end RNA-seq analysis of the 3D evolution of glioma cell populations. Part 2.

  Dataset contains paired-end RNA-seq sequencing data from 221 glioma samples.

  Dataset EGAD00001009497

• Characterization of four subtypes in morphologically normal tissue excised proximal and distal to breast cancer

  RNA sequencing data from breast cancers (n=18) and their matched HN tissues (n=36), healthy breast from cosmetic reduction mammoplasty (RM; n=5), and risk reducing mastectomies (RR, n=5), with peritumoral samples excised proximal to (TP, less than 2 cm) and distal from (TD, 5-10 cm) the primary tumor.

  Dataset EGAD00001006291

• Pre-post neoadjuvant chemotherapy breast cancer dataset- RNAseq data

  This dataset contains RNAseq data of 20 paired pre-post neoadjuvant chemotherapy breast cancer samples. In total the set contains n=20 biopsies, n=20 surgery specimens. Each sample has 2 fastq files, so n=80 fastq files are uploaded in total.

  Dataset EGAD00001008421

• Long read mRNA sequencing of blood cells exposed to different immune stimuli

  Long-read (PacBio) RNA sequencing dataset of in vitro stimulated PBMC cells. 5 samples consisting of 1 RPMI control and 4 stimulus conditions (lipopolysaccharide (LPS), polyI-polyC, S. aureus and C. albicans) all originating from one donor. Files are raw BAM format files generated by Sequel 2 machine.

  Dataset EGAD00001009998

• Exome sequencing of two siblings with a neurodegenerative disorder identifies causative compound heterozygous variants in SLC5A6

  Exome sequencing data of two siblings of with a neurodegenerative phenotype due to SMVT deficiency. Exonic sequences were enriched using the SeqCap EZ Human Exome Library v3.0 kit (Roche NimbleGen) and libraries sequenced as 100bp paired-end reads on the HiSeq 2000 platform (Illumina).

  Dataset EGAD00001005364

• SCLC study MGH - RNAseq dataset

  RNA-seq analyses were performed on cDNA libraries prepared from PolyA+ RNA using the Illumina TruSeq protocol for mRNA. The final libraries were sequenced with a paired-end 2×75 bp protocol aiming at 8.5 Gb per sample for a 30x mean coverage of the annotated transcriptome. All sequencing reactions were conducted on an Illumina HiSeq instrument (Illumina, San Diego, CA, USA).

  Dataset EGAD00001003969

• Paroxysmal Neurological Disorders 2

  We are sequencing the exomes of patients with paroxysmal neurological disorders mainly focusing on migraine and epilepsy. Cases are collected from performance sites of members of the International Headache Genetics consortium and EuroEPINOMICS. Most cases have a strong family history. The study sample will include both cases and controls.

  Dataset EGAD00001000407

• Highly differentiated, fusion-negative rhabdomyosarcoma.

  Sequencing was performed using OncoPanel v.2 (OPv2), an Agilent SureSelect custom designed bait set consisting of the coding regions of 504 genes, previously linked to human cancer. Sequencing wa sperformed on an Illumina HiSeq 2500. 14 highly differentiated, fusion-negative rhabdomyosarcoma tumor samples, and 8 non-matched normal skeletal muscle samples weer sequenced. BAM files are available for download.

  Dataset EGAD00001003746

• Exome sequencing data

  Exome sequencing fastq files from 6 mutation carriers and 5 non-carriers from 2 families. One µg DNA was used for library preparation using the TruSeq DNA LT Sample Prep Kit v2 according to the manufacturer’s instructions (Illumina). Hybridization was performed using Nimblegen SeqCap EZ Exome v3 (Roche) and Paired-end Sequencing (2x100 bp) on the Illumina HiSeq 2000 with TruSeq v3 chemistry (Illumina).

  Dataset EGAD00001003745

• NIHR BioResource Rare Diseases WGS project - Intrahepatic Cholestasis of Pregnancy (ICP) Rare Disease domain

  Short read whole genome sequencing (WGS) CRAM files for the NIHR BioResource Rare Diseases WGS project.Participants from the Intrahepatic Cholestasis of Pregnancy (ICP) Rare Disease domain

  Dataset EGAD00001004515

• Complete Metagenomics from feces

  Complete Microbiome Metagenomics from feces of 461 IBD patients; The sequencer used was the Illumina HiSeq 2000 with a paired end reads design, reflected in the 2 FastQ format files per sample.

  Dataset EGAD00001004194

• Dataset Gene-Breakpoint Panel

  In this study we analysed patients with metastatic prostate cancer to scan their tumor genomes noninvasively in plasma DNA. We enriched 1.3 Mbp of seven plasma DNAs (4 CRPC cases: CRPC1-3 and CRPC5; 3 CSPC cases: CSPC1-2 and CSPC4) including exonic sequences of 55 cancer genes and 38 introns of 18 genes, where fusion breakpoints have been described using Sure Select Custom DNA Kit.

  Dataset EGAD00001000365

• ECCO-GEN Valve Methylation Dataset (non-diseased)

  The valve methylation dataset consists of 12 bam files of human non-diseased valve tissue samples that are free from calcification (6 aortic and 6 mitral valves - matched; 10 males: 2 females; age range 42 – 64 years, mean age 52.2 years, SD 9.9682). Donor hearts are free from cardiovascular and valvular complications.

  Dataset EGAD00001006303

• Amplicon sequencing of IPC-298 and MelJuso parental cell lines and Belvarafenib resistant IPC-298 colony

  Amplicon seqeuencing of (1) wildtype IPC298 cell line grown for 3-4 weeks with DMSO, amplified for ARAF exon 11 (2) IPC298 cells treated for 3-4 weeks with 10uM belvarafenib, isolated colony 9, amplified for ARAF exon 11 (3) MelJuso cell line grown with DMSO, amplified for ARAF exon 11

  Dataset EGAD00001007061

• ChIP-seq bulk

  This dataset gather ChIP-seq data produced by immunoprecipitating CTCF factor in own laboratory in MM.1S cell line in EtOH and Dex conditions. It also gather ChIP-seq dataset produced by external laboratory (Active Motif) for H3K27ac mark and GR transcription factor in same cell line and conditions ( MM.1S ETOH/Dex)

  Dataset EGAD00001011136

• HSC_population_dynamics___KX004_samples___WGS

  My research project aims to use the clonal dynamics of spontaneously occurring somatic mutations to answer fundamental questions about human haematopoietic stem cell (HSC) biology. The four major questions I will address are: 1. How do age and aging affect normal human HSC dynamics in vivo? 2. How do in vivo perturbations, particularly chemotherapy and increased levels of reactive oxygen species, affect HSC population dynamics? 3. Is response to in vitro perturbation heritable and/or correlated with other features such as age of individual and contribution of the lineage to peripheral blood? 4. How are HSC dynamics altered in people with early driver mutations (clonal haematopoiesis)?

  Study EGAS00001003768

• HSC_population_dynamics___CB002_samples

  My research project aims to use the clonal dynamics of spontaneously occurring somatic mutations to answer fundamental questions about human haematopoietic stem cell (HSC) biology. The four major questions I will address are: 1. How do age and aging affect normal human HSC dynamics in vivo? 2. How do in vivo perturbations, particularly chemotherapy and increased levels of reactive oxygen species, affect HSC population dynamics? 3. Is response to in vitro perturbation heritable and/or correlated with other features such as age of individual and contribution of the lineage to peripheral blood? 4. How are HSC dynamics altered in people with early driver mutations (clonal haematopoiesis)?

  Study EGAS00001003743

• HSC_population_dynamics___KX007_samples

  My research project aims to use the clonal dynamics of spontaneously occurring somatic mutations to answer fundamental questions about human haematopoietic stem cell (HSC) biology. The four major questions I will address are: 1. How do age and aging affect normal human HSC dynamics in vivo? 2. How do in vivo perturbations, particularly chemotherapy and increased levels of reactive oxygen species, affect HSC population dynamics? 3. Is response to in vitro perturbation heritable and/or correlated with other features such as age of individual and contribution of the lineage to peripheral blood? 4. How are HSC dynamics altered in people with early driver mutations (clonal haematopoiesis)?

  Study EGAS00001004193

• HSC_population_dynamics___KX008_samples

  My research project aims to use the clonal dynamics of spontaneously occurring somatic mutations to answer fundamental questions about human haematopoietic stem cell (HSC) biology. The four major questions I will address are: 1. How do age and aging affect normal human HSC dynamics in vivo? 2. How do in vivo perturbations, particularly chemotherapy and increased levels of reactive oxygen species, affect HSC population dynamics? 3. Is response to in vitro perturbation heritable and/or correlated with other features such as age of individual and contribution of the lineage to peripheral blood? 4. How are HSC dynamics altered in people with early driver mutations (clonal haematopoiesis)?

  Study EGAS00001004490

• HSC_population_dynamics_CBD_samples

  My research project aims to use the clonal dynamics of spontaneously occurring somatic mutations to answer fundamental questions about human haematopoietic stem cell (HSC) biology. The four major questions I will address are: 1. How do age and aging affect normal human HSC dynamics in vivo? 2. How do in vivo perturbations, particularly chemotherapy and increased levels of reactive oxygen species, affect HSC population dynamics? 3. Is response to in vitro perturbation heritable and/or correlated with other features such as age of individual and contribution of the lineage to peripheral blood? 4. How are HSC dynamics altered in people with early driver mutations (clonal haematopoiesis)?

  Study EGAS00001003091

• HSC_population_dynamics___KX003_samples

  My research project aims to use the clonal dynamics of spontaneously occurring somatic mutations to answer fundamental questions about human haematopoietic stem cell (HSC) biology. The four major questions I will address are: 1. How do age and aging affect normal human HSC dynamics in vivo? 2. How do in vivo perturbations, particularly chemotherapy and increased levels of reactive oxygen species, affect HSC population dynamics? 3. Is response to in vitro perturbation heritable and/or correlated with other features such as age of individual and contribution of the lineage to peripheral blood? 4. How are HSC dynamics altered in people with early driver mutations (clonal haematopoiesis)?

  Study EGAS00001003550

• HSC_population_dynamics___TG001_2_samples

  My research project aims to use the clonal dynamics of spontaneously occurring somatic mutations to answer fundamental questions about human haematopoietic stem cell (HSC) biology. The four major questions I will address are: 1. How do age and aging affect normal human HSC dynamics in vivo? 2. How do in vivo perturbations, particularly chemotherapy and increased levels of reactive oxygen species, affect HSC population dynamics? 3. Is response to in vitro perturbation heritable and/or correlated with other features such as age of individual and contribution of the lineage to peripheral blood? 4. How are HSC dynamics altered in people with early driver mutations (clonal haematopoiesis)?

  Study EGAS00001003688

• PGRN/PAT: The genomic basis for susceptibility to drug-induced long QT syndrome (diLQTS)

  The goal of this study was to search for genetic variants that could be responsible for modifying the risk of drug-induced long QT syndrome (diLQTS). diLQTS is a relatively common adverse drug event and has been a leading cause for drug relabeling and withdrawal from the market. Our hypothesis, that variants in genes which regulate electrical properties in the heart modify the risk of diLQTS, was tested by sequencing approximately 225 patients of European descent using next-generation targeted captured or whole exome sequencing. Data from cases and controls (1:2) were analyzed to identify both rare and common genetic variation.

  Study phs000808

• Gene Expression Signatures in CATHGEN

  Case control cohort: The details have been previously published: American Heart Journal. 2010;160:371-379 e372. Briefly, a nested case:control cohort of CATHGEN participants who had experienced death or MI (n = 250) after their index catheterization and age-, sex-, and race-matched controls (n = 250) who were free of death/MI > 2 years after cardiac catheterization was identified as part of the MURDOCK Horizon 1 Cardiovascular Disease Study.21 Sufficient RNA for microarray analysis was available in 447 members of this cohort. Observational cohort: 224 sequential CATHGEN samples were selected for whole blood RNA analysis, of which, 191 had sufficient RNA for microarray analysis.

  Study phs000551

• Genetic Basis of Cryptorchidism

  Non-syndromic cryptorchidism is a common malformation, but the genetic loci that increase susceptibility to cryptorchidism remain unknown. A genome-wide association study (GWAS) was completed to determine whether common allelic variants are associated with susceptibility to cryptorchidism. Two sets of discovery groups were genotyped. Group 1 (559 cases and 1772 controls) was genotyped with HumanHap550v1.0, HumanHap550v3.0 or Human610-quad v1.0. Group 2 (353 cases and 1149 controls) was genotyped with HumanOmniExpress-12v1 or HumanOmniExpress-12v1-1. The sample and marker QCs were performed separately using PLINK (v1.07; http://pngu.mgh.harvard.edu/purcell/plink/) and logistic regression analyses were performed with first and second multidimensional scaling (MDS) components as covariates.

  Study phs000986

• Single-Cell RNA-Sequencing Analysis of Responses to Pembrolizumab in Sezary Syndrome

  This phase 2 single arm clinical trial assessed the efficacy of pembrolizumab in patients with previously treated mycosis fungoides or Sezary syndrome. Pembrolizumab was found to have a 38% overall response rate, and a 27% overall response rate in subjects with Sezary syndrome. We performed single-cell RNA-sequencing on samples collected before the first treatment and after 3 weeks of pembrolizumab treatment. Sequencing was performed on cryopreserved peripheral blood T-lymphocytes isolated from 6 trial participants, including 3 patients who responded to pembrolizumab treatment and 3 patients who did not respond. A total of 118,961 peripheral blood T-cells are included in this data set.

  Study phs002933

• Somatic Copy Number Analysis of Endometrial Carcinomas

  Endometrial cancer (EC) is the most commonly diagnosed gynecologic malignancy in the United States and is the sixth leading cause of cancer death amongst American women. The purpose of this study was to identify somatic (tumor-specific) copy number alterations in 7 clear cell ECs, 31 serous ECs, 17 endometrioid ECs, and the clear cell components of 2 endometrioid/clear cell ECs. To this end, DNAs from de-identified primary endometrial tumors and matched non-tumor tissues or blood were hybridized to high-density Illumina Infinium HumanHap650Y Beadchips or to high-density Human660W-Quad Beadchips and the data analyzed to annotate somatic copy number alterations throughout the genome.

  Study phs001690

• NHLBI TOPMed: Genetics of Asthma in Latino Americans (GALA)

  This is a case pharmacogenetic study of bronchodilator drug response (Albuterol) among racially admixed Latino children with asthma between the ages of 8-40. Lung function testing was performed using the KoKo PFT system and each participant was administered albuterol dependent on age. Participants under 16 years of age, were administered 2 puffs of albuterol from a standard metered dose inhaler and 4 puffs for participants over 16 years old. The overall goal is to identify genetic factors which are predictive of drug response in children with asthma. The principal tools include a questionnaire and biological specimen collection. Participants with asthma have physician-diagnosed asthma, symptoms and medications.

  Study phs001542

• Collaborative Cohort of Cohorts for COVID-19 Research (C4R): Severe Asthma Research Program (SARP)

  Cohort Description The Severe Asthma Research Program (SARP) has been investigating the clinical, physiologic and molecular phenotypes of asthma since 2000. It is currently following ~400 deeply phenotyped asthma patients. Data Being Submitted Wave 1 questionnaire data includes 397 variables for up to 375 SARP participants in C4R.Wave 2 questionnaire data includes 448 variables for up to 289 SARP participants in C4R.Dried Blood Spot/Serosurvey data includes 7 variables for up to 290 SARP participants in C4R.Derived data includes 43 variables for up to 463 SARP participants in C4R.Phenotype data includes 113 variables for up to 463 SARP participants in C4R.

  Study phs002913

• HSC_population_dynamics___PX001_samples

  My research project aims to use the clonal dynamics of spontaneously occurring somatic mutations to answer fundamental questions about human haematopoietic stem cell (HSC) biology. The four major questions I will address are: 1. How do age and aging affect normal human HSC dynamics in vivo? 2. How do in vivo perturbations, particularly chemotherapy and increased levels of reactive oxygen species, affect HSC population dynamics? 3. Is response to in vitro perturbation heritable and/or correlated with other features such as age of individual and contribution of the lineage to peripheral blood? 4. How are HSC dynamics altered in people with early driver mutations (clonal haematopoiesis)?

  Study EGAS00001004146

• HSC_population_dynamics___KX009_samples

  My research project aims to use the clonal dynamics of spontaneously occurring somatic mutations to answer fundamental questions about human haematopoietic stem cell (HSC) biology. The four major questions I will address are: 1. How do age and aging affect normal human HSC dynamics in vivo? 2. How do in vivo perturbations, particularly chemotherapy and increased levels of reactive oxygen species, affect HSC population dynamics? 3. Is response to in vitro perturbation heritable and/or correlated with other features such as age of individual and contribution of the lineage to peripheral blood? 4. How are HSC dynamics altered in people with early driver mutations (clonal haematopoiesis)?

  Study EGAS00001004580

• HSC_population_dynamics___KX010_samples

  My research project aims to use the clonal dynamics of spontaneously occurring somatic mutations to answer fundamental questions about human haematopoietic stem cell (HSC) biology. The four major questions I will address are: 1. How do age and aging affect normal human HSC dynamics in vivo? 2. How do in vivo perturbations, particularly chemotherapy and increased levels of reactive oxygen species, affect HSC population dynamics? 3. Is response to in vitro perturbation heritable and/or correlated with other features such as age of individual and contribution of the lineage to peripheral blood? 4. How are HSC dynamics altered in people with early driver mutations (clonal haematopoiesis)?

  Study EGAS00001004581

• Understanding Rare Variant Contributions to autism: Lessons from Dystrofin-Deficient Model

  This project generated a whole-exome sequencing (WES) dataset of 83 boys with a pathogenic variant in the DMD gene, along with WES data from the parents of 38 of them, totaling 159 samples. Pathogenic DMD variants, besides causing dystrophinopathies, are also known risk factors for neurodevelopmental disorders (NDDs). However, the low penetrance of NDDs in individuals with dystrophinopathies suggests that additional factors contribute to their manifestation. This study aimed to: (1) characterize ASD in males with dystrophinopathies; (2) determine the relevance of additional de novo and inherited rare risk variants for their neurodevelopmental phenotype; and (3) clinically and functionally characterize the identified risk variants.

  Study EGAS50000000754

• Genomic analysis of head and neck squamous cell carcinoma upon acquired resistance to cetuximab

  Anti-epidermal growth factor receptor (EGFR) monoclonal antibodies (cetuximab) remain the only FDA-approved targeted therapy for patients with recurrent/metastatic head and neck squamous cell carcinoma (HNSCC). Unfortunately, most patients develop acquired resistance to cetuximab and there is currently no further therapeutic option for these patients (unmet clinical need), thereby highlighting the need to better understand resistance-causing mechanisms. Here, we carried out whole-exome sequencing on 2 cetuximab-sensitive and -resistant patient-derived xenograft models of HNSCC. Our data reveal several genetic alterations (mutations and copy number variations) associated with acquired resistance to anti-EGFR therapy.

  Study EGAS50000000800

• NHLBI TOPMed: Chicago Initiative to Raise Asthma Health Equity (CHIRAH)

  The CHIRAH project was a community-based study of the factors associated with asthma morbidity in the African American population. CHIRAH evaluated the role of various variables (biologic/environmental, psychologic/behavioral, and socioeconomic) on asthma morbidity and the function of changes in these variables on asthma morbidity in a longitudinal fashion. This involved collection of a cohort-based on school screening which was sampled to include similar numbers of underprivileged and non-underprivileged subjects which roughly equally represented self-reported African Americans and self-reported non-African Americans. Subjects were followed up every 3 months of this cohort over the course of 2 years.

  Study phs001605

• HSC_population_dynamics_KSP_samples

  My research project aims to use the clonal dynamics of spontaneously occurring somatic mutations to answer fundamental questions about human haematopoietic stem cell (HSC) biology. The four major questions I will address are: 1. How do age and aging affect normal human HSC dynamics in vivo? 2. How do in vivo perturbations, particularly chemotherapy and increased levels of reactive oxygen species, affect HSC population dynamics? 3. Is response to in vitro perturbation heritable and/or correlated with other features such as age of individual and contribution of the lineage to peripheral blood? 4. How are HSC dynamics altered in people with early driver mutations (clonal haematopoiesis)?

  Study EGAS00001002762

• Amplicon sequencing of melanoma samples

  The types of biomarkers for skin tumors have been 1) biochemical markers in blood, urine, and body fluid, 2) histopathological markers, 3) genetic examination of tumor tissue, 4) tumor-susceptibility assessed by germ_x0002_line genetic examination. Biomarkers in a blood are frequently used in the treatment of cutaneous malignancies, but are not suitable for early detection of malignancies. Research on circulating tumor cells, cell free DNA, exosomes has been promoted in recent years, but clinical application is halfway. Based on these circumstances, the purpose of this study is to search for biomarkers for diagnosis, therapeutic effect, and follow-up of skin tumors, and to verify their usefulness.

  Study JGAS000351

• GOSH_Paediatric_Tumour_23P108_WSSS_WGS_Managed_Access

  We have a case of two siblings (twins) who were born with nodular blue rashes over their body. The first twin had a large periorbital subcutaneous mass which was diagnosed as infantile undifferentiated sarcoma. This baby was too systematically unwell for chemotherapy and died at 12 days of age. The second sibling received two cycles of emergency chemotherapy however died due to disease progression and secondary haemorrhage at 2 months of age. Post-mortem normal and tumour samples have been taken. In addition to placental tissue and parental germline DNA, the goal will be to investigate intra-uterine transfer of sarcoma and the phylogenetic relationship of tumours in both twins.

  Study EGAS00001007536

• Study for establishment for effective screening and diagnosis of Lynch syndrome

  The purpose of this study is to establish efficient diagnostic procedure of the Lynch syndrome in Japan and to determine the MMR gene mutation spectrum and clinicopathologic characteristics.The person who is suspected Lynch Syndrome and gives informed consent for participation in this study .To carry out the project ?Construction of clinical and genetic integral information database to help Lynch syndrome management?, the following three are required. 1) screening for Lynch syndrome-suspected cases, 2) genetic testing to define Lynch syndrome, 3) integration of detailed clinical data of Lynch syndrome, and 4) The case which has not been diagnosed Lynch syndrome, is investigated causing gene.

  Study JGAS000638

• Spatial and temporal genomic evolution in glioblastoma

  Tumor heterogeneity is a challenging barrier to successful targeted therapy in glioblastoma. Identifying the mechanisms that drive cancer cells as they genetically evolve and adapt in response to treatment is a vital goal of modern cancer research. Analysis of sequencing data provides a method for uncovering the mechanisms sustaining tumor heterogeneity and driving evolution. Here, we analyzed genomic profiles of GBM biopsies taken from pre- and post-treatment GBMs (with matched germline controls), to understand 1) the intratumoral clonal compositions of primary GBM and 2) how GBM responds to therapeutic intervention. Our results provide a molecular portrait of GBM recurrence.

  Study EGAS00001001033

• Mutational signatures in head and neck cancer (H019)

  Genomic alterations are a driving force in the multistep process of head and neck cancer (HNC) and result from the interaction of exogenous environmental exposures and endogenous cellular processes. Each of these processes leaves a characteristic pattern of mutations on the tumor genome providing the unique opportunity to decipher specific signatures of mutational processes operative during HNC pathogenesis and to address their prognostic value. Computational analysis of whole exome sequencing data of the HIPO-HNC (n=83) and TCGA-HNSC (n=506) cohorts revealed five common mutational signatures (COSMIC signature 1, 2, 3, 13 and 16), and demonstrated their significant association with etiological risk factors (tobacco, alcohol and HPV16).

  Study EGAS00001004588

• HSC_population_dynamics___CB001_samples

  My research project aims to use the clonal dynamics of spontaneously occurring somatic mutations to answer fundamental questions about human haematopoietic stem cell (HSC) biology. The four major questions I will address are: 1. How do age and aging affect normal human HSC dynamics in vivo? 2. How do in vivo perturbations, particularly chemotherapy and increased levels of reactive oxygen species, affect HSC population dynamics? 3. Is response to in vitro perturbation heritable and/or correlated with other features such as age of individual and contribution of the lineage to peripheral blood? 4. How are HSC dynamics altered in people with early driver mutations (clonal haematopoiesis)?

  Study EGAS00001003397

• HSC_population_dynamics___LEUK4_samples

  My research project aims to use the clonal dynamics of spontaneously occurring somatic mutations to answer fundamental questions about human haematopoietic stem cell (HSC) biology. The four major questions I will address are: 1. How do age and aging affect normal human HSC dynamics in vivo? 2. How do in vivo perturbations, particularly chemotherapy and increased levels of reactive oxygen species, affect HSC population dynamics? 3. Is response to in vitro perturbation heritable and/or correlated with other features such as age of individual and contribution of the lineage to peripheral blood? 4. How are HSC dynamics altered in people with early driver mutations (clonal haematopoiesis)?

  Study EGAS00001004247

• Small intestinal plasma cells transcriptome profiles

  Objective: Plasma cells (PCs) are terminally differentiated B-lymphocytes that produce antibodies. The lamina propria of the small intestine is particularly rich in PCs. In coeliac disease (CeD) there is infiltration and increased density of PCs in the small intestinal lesion. Many of these PCs produce disease-specific autoantibodies targeting the enzyme transglutaminase 2 (TG2). The plasmacytosis and high numbers of disease-antigen reactive PCs in CeD motivated us to study the transcriptional programme of PCs from coeliac gut lesions. Design: We performed RNASeq analysis of IgA+ PCs of untreated CeD patients being specific or non-specific for TG2 and from healthy controls.

  Study EGAS00001003345

• RNA-seq of uncultured CD112high and CD112low long-term(LT) human hematopoietic stem cells (HSC) and cultured and lentiviral transduced (CTRL, INKA1-OE) LT- and short-term HSC from umbilical cord blood

  We performed RNA-sequencing to elucidate the biological pathways (1) altered by INKA1 overexpression in LT-HSC and ST-HSC that may contribute to the induced transient restraint in generating proliferative hematopoietic output in vivo and in vitro; and (2) that underlie the differential in vitro priming and regeneration phenotypes of CD112high and CD112low LT-HSC. Therefore, we prospectively isolated indicated subpopulations from 3 independent human umbilical cord blood pools and subjected them either to RNA-sequencing directly or following culture, lentiviral transduction and purification of the transduced cell fractions.

  Study EGAS00001004768

• Spatially resolved antigen receptor and gene expression data from human tonsil tissue

  The dataset includes spatially-resolved gene expression and antigen receptor data from two Tonsil samples (1 and 2). Tissue sections from the tonsil samples were used for spatial transcriptomics (Visium, 10x genomics). Tonsil 2 tissue sections were analyzed by a new method (Spatial VDJ) to spatially resolve antigen receptor sequences (target capture), which was developed in our publication. Nearby or adjacent tissue sections (from Tonsil2) were also analyzed by a bulk antigen receptor sequencing approach (amplicon sequencing), by a method also newly developed by us in the same publication (Bulk SS3 VDJ). For Visium, the data were anonymized (all SNPs removed) using Bamboozle (Ziegenhain and Sandberg, Nature Communications 2021). The deposited data is in the form of fastq files. All remaining data, metadata, micrographs of the tissue sections (of those used for spatial transcriptomics), and scripts used for the analysis are available at Zenodo (DOI: 10.5281/zenodo.7961605). Final libraries were sequenced on NextSeq2000 (Illumina) or NovaSeq6000 (Illumina) and analyzed with Seurat, Space Ranger, and STutility pipelines.

  Dataset EGAD00001011062

• Health and Retirement Study (HRS)

  Introduction to V2: This data release comprises data from the V1 release combined with approximately 3,000 additional samples, collected during the HRS 2010 field period. The 2010 data include samples from a random half of the new cohort enrolled in 2010 along with a significant expansion of the minority sample. Description: The University of Michigan Health and Retirement Study (HRS) is a longitudinal panel study that surveys a representative sample of approximately 20,000 people in America over the age of 50 every two years. Supported by the National Institute on Aging (NIA U01AG009740) and the Social Security Administration, the HRS explores the changes in labor force participation and the health transitions that individuals undergo toward the end of their work lives and in the years that follow. The study collects information about income, work, assets, pension plans, health insurance, disability, physical health and functioning, cognitive functioning, and health care expenditures. Through its unique and in-depth interviews, the HRS provides an invaluable and growing body of multidisciplinary data that researchers can use to address important questions about the challenges and opportunities of aging. Because of its innovation and importance, the HRS has become the model and hub for a growing network of harmonized longitudinal aging studies around the world. Origins of the HRS. As the population ages it is increasingly important to obtain reliable data about aging and topics that are relevant to a range of policy issues in aging. To address this need, the National Institutes on Aging (NIA) established a cooperative agreement with the University of Michigan Institute for Social Research to collect such data. The HRS launched data collection in 1992 and has re-interviewed the original sample of respondents every two years since then. By adding new cohorts and refreshing the sample, the HRS has grown to become the largest, most representative longitudinal panel study of Americans 50 years and older. HRS Study Design. The target population for the original HRS cohort includes all adults in the contiguous United States born during the years 1931-1941 who reside in households, with a 2:1 oversample of African-American and Hispanic populations. The original sample is refreshed with new birth cohorts (51-56 years of age) every six years. The sample has been expanded over the years to include a broader range of birth cohorts as well. The target population for the AHEAD survey consists of United States household residents who were born in 1923 or earlier. Children of the Depression (CODA) recruits households born 1924-1930, War Babies 1942-47, Early Boomers 1948-53, and Mid-Boomers 1954-59. Data collection includes a mixed mode design combining in-person, telephone, mail, and Internet. For consenting respondents, HRS data are linked at the individual level to administrative records from Social Security and Medicare claims. Genetic Research in the HRS. The HRS has genotyped 2.5 million single nucleotide polymorphisms (SNPs) on respondents using Illumina's Human Omni2.5-Quad (Omni2.5) BeadChip. The genotyping was performed by the NIH Center for Inherited Disease Research (CIDR). Saliva was collected on half of the HRS sample each wave starting in 2006. In 2006, saliva was collected using a mouthwash collection method. From 2008 onward, the data collection method switched to the Oragene kit. Saliva completion rates were 83% in 2006, 84% in 2008, and 80% in 2010 among new cohort enrollees. HRS Phenotypic data. Phenotypic data are available on a variety of dimensions. Health measures include physical/psychological self-report, various health conditions, disabilities, cognitive performance, health behaviors (smoking, drinking, exercise), physical performance and anthropomorphic measures, and biomarkers (HbA1c, Total Cholesterol, HDL, CRP, Cystatin-C). Data are also available on health services including utilization, insurance and out-of-pocket spending with linkage to Medicare records. Economic measures include employment status/history, earnings, disability, retirement, type of work, income by source, wealth by asset type, capital gains/debt, consumption, linkage to pensions, Social Security earnings/benefit histories. There is also extensive information on family structure, proximity, transfers to/from of money, time, social and psychological characteristics, as well as a wide range of demographics. Performance on a cognitive test combining immediate and delayed word recall was selected as an example trait for the dbGaP data release. In the immediate word recall task the interviewer reads a list of 10 nouns to the respondent and asks the respondent to recall as many words as possible from the list in any order. After approximately five minutes of asking other survey questions, the respondent is asked to recall the nouns previously presented as part of the immediate recall task. The total recall score is the sum of the correct answers to these two tasks, with a range of 0 to 20. Researchers who wish to link to other HRS measures not in dbGaP will be able to apply for access from HRS. A separate Data Use Agreement (DUA) will be required for linkage to the HRS data. See the HRS website (http://hrsonline.isr.umich.edu/gwas) for details.

  Study phs000428

• A Study to Assess the Cardiovascular, Cognitive, and Subjective Effects of Atomoxetine in Combination with Intravenous Methamphetamine

  The Study to Assess the Cardiovascular, Cognitive, and Subjective Effects of Atomoxetine in Combination with Intravenous Methamphetamine started in 2007 and ended in 2011. It was a small pilot study that included methamphetamine abusing individuals and healthy control participants aged 18-50 years. Participants who qualified over the telephone were scheduled to visit the London Laboratory at the UCLA Semel Institute for Neuroscience and Human Behavior for the In-Person Screening Phase. The screening procedures, usually scheduled over two visits, determined if participants were eligible to complete the subsequent study visits. Both groups completed identical screening procedures, including a SCID diagnostic interview to rule out any major psychiatric disorders. Methamphetamine users also answered questionnaires specific to their drug use. Urine toxicology for marijuana, opiates, cocaine, methamphetamine, and benzodiazepines were monitored at the beginning and throughout the study. Additionally, participants had blood samples to test for Rapid Plasma Reagin (exposure to syphilis), purified protein derivative (PPD), HIV and Hepatitis-C (HCV). Positive test results were relayed by a study physician and resulted in termination from continuing in the study. The inpatient portion of the study lasted a total of 24 days. To confirm compliance with abstinence from illicit and prescription drug use for the duration of the study, urine and breath alcohol testing was performed for both inpatient (methamphetamine users) and outpatient (healthy control) groups. Each subject was randomized to receive either atomoxetine (80 mg daily) or placebo. During inpatient days of the study, a study physician oversaw research subjects daily and experimental procedures were conducted in the General Clinical Research Center (GCRC). During drug administration sessions, heart rate and blood pressure were assessed at frequent intervals. Experimental sessions lasted around three hours and were conducted at approximately the same time of day for a given participant. Lunch was provided to participants at 11:30am with the prohibition of caffeine on study days involving methamphetamine administration. Participants were provided with smoke breaks as needed to assure that acute nicotine withdrawal did not negatively impact performance on cognitive testing. The following outlines the day to day procedures for a methamphetamine inpatient: Phase I Inpatient Study (15 days total) Days 1-3: On the day of admission, participants received blood tests and an EKG in order to determine that they had no occult medical conditions which would make their participation in the study medically contraindicated. A three day washout period was provided at the beginning of the study to establish an appropriate methamphetamine-free baseline for testing. Days 4-6: Participants completed cognitive test batteries to assess inhibitory control including self-report measures and cognitive testing, as well as up to three MRI scanning sessions. Day 7: On day 7, at 9AM and 1PM, participants received methamphetamine in a single-blinded condition. It was administered as two IV infusions of 15mg separated by a 60min break. The total dose of IV methamphetamine was 30mg. Participants were clinically evaluated by continuous cardiac telemetry, serial EKG and measurement of vital signs, during and after infusions, in order to determine the medical safety of methamphetamine infusion in the absence of study medication. Day 8: On day 8 we evaluated the safety and residual effects of the methamphetamine administered on the previous day. Days 9-10: After demonstrating medical and psychiatric stability of the initial methamphetamine infusion, participants were then randomized to receive placebo or atomoxetine (0 or 40mg) under double-blind conditions, which would be given at 8AM on both study days. Days 11-12: On days 11 and 12, participants remained in the GCRC and took two doses of test compound atomoxetine (0 or 40mg) at 8AM and 8PM. On the morning of day 12, participants completed a series of cognitive testing. Day 13: On day 13, participants remained in the GCRC, and took two doses of the test compound atomoxetine (0 or 40mg) at 8AM and 8PM. At 9AM and noon, they received methamphetamine under double-blind conditions administered non-contingently as two infusions of 0 or 15mg by IV (intravenously), with each infusion separated by 60min. The total dose of IV methamphetamine that each participant received was 30mg. As before, participants were clinically evaluated by continuous cardiac telemetry, serial EKG and measurement of vital signs, during and after infusions, in order to determine the medical safety of methamphetamine infusion in those participants receiving study medication. Day 14: On day 14 at 8AM, participants received their final dosing of the first test compound (atomoxetine 0 or 40mg). At 9AM and 1PM, participants selected between methamphetamine infusion or money using double-blind conditions in a multiple-choice self-administration paradigm. Participants were able to take up to two infusions of 0 or 15mg of methamphetamine, separated by 60min. The total dose of IV methamphetamine that each participant received on day 14 was 30mg. Participants were clinically evaluated by continuous cardiac telemetry, serial EKG and measurement of vital signs, during and after infusions, in order to determine the medical safety of methamphetamine infusion in those participants receiving study medication. At 5pm on day 14 discharge laboratory studies were drawn. Day 15: On day 15, a final EKG was performed as well as a review of discharge laboratory studies, including review of the EKG and continued medical and psychiatric stability. Upon clearance from a physician, participants were discharged on day 15. Participants spent at least 2 weeks (14 days) out of the hospital prior to returning to the UCLA GCRC for inpatient Phase II. Phase II Inpatient Study (9 days total) Day 1-2: On the day of re-admission, participants received blood tests and an EKG. A two day washout period was provided at the beginning of the study to establish an appropriate methamphetamine free condition for safe administration of the second test compound condition. Days 3-4: On days 3 and 4, given medical stability, participants were then switched to the opposite test compound (atomoxetine 0 or 40mg) under double-blind conditions, in the same manner as in Days 9-10 in Phase I. Days 5-6: Same procedure as in Days 11-12 in Phase I but with opposite medication condition. Day 7: Same procedure as in Day13 in Phase I but with opposite medication condition. Day 8: Same procedure as in Day14 in Phase I but with opposite medication condition. Day 9: Same procedure as in Day14 in Phase I but with opposite medication condition. For healthy control participants, the study consisted of 30 days or fewer of out-patient testing. Healthy control participants had an extensive screening, including a history and physical exam performed by a study physician, an EKG, and laboratory studies performed to assess for medical or psychiatric conditions. Control participants meeting criteria were invited back to UCLA to undergo cognitive testing, and some participants received fMRI scans. Participants were required to refrain from illicit and prescription drug use for the duration of the study, which was confirmed with urine toxicology and breath alcohol level testing on examination days. Caffeine was restricted on study days for least 2 hours prior to cognitive testing and MRI scans. Participants were permitted to drink their normal daily intake of caffeine, given the caveat above. On study days, cigarette smoking was permitted to match conditions used with methamphetamine users. The incorporation of smoke breaks during the test day assured that acute nicotine withdrawal did not negatively impact performance on cognitive tests or neuroimaging. The following outlines procedures for healthy control participants: For normal controls, participation involved one day of outpatient screening, and one day of baseline cognitive testing and possible MRI scans. After these procedures were completed, participants were randomized to the first test compound (atomoxetine 40mg or placebo), to be taken once daily in the morning for 2 days. It was then increased to twice daily for the next 3 days, followed by a final dose (40mg or placebo) on the sixth day of study medication. Participants were also asked to bring their pill packages to assess compliance with the study medication. Additionally, control participants completed a series of repeated-measures cognitive testing (on placebo or atomoxetine, respectively) and possibly two fMRI sessions (separated by a short break). After at least a four-day washout period, control participants were instructed to start the opposite test compound (atomoxetine 40mg or placebo), again to be taken once daily in the morning for two days, then twice daily for 3 days, reaching the final dose (40mg or placebo) of the second test compound in the morning. Participants were again asked to bring their pill packages to assess compliance and had blood drawn to assess atomoxetine levels. Control participants then completed another series of cognitive testing and fMRI testing sessions. They were subsequently discharged from the study. Normal control participants returned two weeks after completion of both study phases in order to complete assessments to their physical and psychological status following treatment.

  Study phs001195

• Single cell RNA-seq and ATAC-seq of CD4+ T cells from blood and tumor of NSCLC patients

  This dataset contains fastq files for paired blood-tumor scRNA-seq samples from 5 NSCLC patients and paired blood-tumor scATAC-seq samples from 2 NSCLC patients, both sequenced with NovaSeq or Illumina HiSeq - Rapid Run.

  Dataset EGAD50000000424

• Disease recurrence after pathologic response

  In this study we aim to gain insight into the mechanisms of immune evasion after initial pathologic response to neoadjuvant immune checkpoint inhibition in macroscopic stage III melanoma by pooling data of the neoadjuvant OpACIN, OpACIN-neo and PRADO trials. Therefore we analyzed in-depth paired baseline(n=10) and recurrent tumor samples of the lymph nodes(n=10) and brain metastasis (n=2) through Whole Exome Sequencing (WES) analyses.

  Dataset EGAD50000000700

• Dataset of Sarcopenia HNSCC

  For this study, we compared the transcriptome of samples exposed to the influence of the FaDu cells (N=6) vs in the control condition (N=2). Muscle fragments were collected intraoperatively from patients with HNSCCs (N=9). The collection of these samples was made possible as part of an ancillary study linked to the Magnolia clinical trial (NCT 04842162). These fragments most often came from the sternocleidomastoid muscle.

  Dataset EGAD50000000944

• Tumor Profiler Project - OV scDNA data additional samples

  The dataset contains 10x Chromium single-cell DNA sequencing data from 6 samples from 5 different patients with ovarian cancer. 4 samples were collected from the tumor, and 2 samples from ascites. Sequencing was performed in paired-end mode and sequencing data is provided in fastq format. This dataset contains additional samples from patients not classified as having high-grade serous adenocarcinoma.

  Dataset EGAD50000001294

• RNA sequencing of baseline HCC PDX models

  To establish the baseline transcriptional profiles, we performed bulk RNA-seq for 36 of our HCC PDX models. 2-6 samples were collected for each model resulting in a total of 68 samples. Isolated RNA was used as input for library preparation using TruSeq RNA Sample Preparation Kit v2 (Illumina). The libraries were multiplexed and sequenced on Illumina HiSeq 2500 (Illumina) to produce FASTQ files.

  Dataset EGAD50000000736

• single-cell RNA-seq profiling of 2 patient derived colorectal cancer organoids after treatment with a combination of different anticancer drugs

  This dataset consists of single-cell RNA-seq profiling of colorectal cancer organoids derived from two patients. The organoids were profiled both after 4 weeks of treatment and after a drug holiday of two weeks. There are 49 RNA sequence files generated using single cell RNA sequencing technology from 10X genomics.

  Dataset EGAD50000001495

• Mate Pair Sequencing data for Molecular Characterization of ETMRs

  This dataset contains Mate Pair Sequencing data from 15 samples from 13 patients. Mate pair DNA library preparation was carried out using the Illumina MP v.2 reagents and protocol. In brief, fragmentation of genomic DNA was performed using a Hydroshear device to an insert size of 4.5 kb followed by sequencing with Illumina HiSeq 2000 instruments resulting in 30 Fastq files (paired end).

  Dataset EGAD00001006207

• BLUEPRINT release August 2016, Bisulfite-Seq for thymocyte, on genome GRCh38

  Bisulfite-Seq data for 1 thymocyte sample(s). 14 run(s), 1 experiment(s), 2 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816

  Dataset EGAD00001002440

• Reference single cell SNP array dataset from Coriell for training and validation of method for accurate single cell genotyping

  This dataset contains DNA from B-lymphocytes from 2 Coriell families and 4 individuals hybridized to HumanKaryomap BeadChip Array. Single cells from subjects GM12878 and GM7228 were amplified using multiple displacement amplification (SureMDA) according to Infium Karyomapping Assay Guide. Bulk DNA was processed and hybridized to an array for subject GM12878, GM07224 and GM07225.

  Dataset EGAD00001006376

• Single-cell transcriptome sequencing

  Raw reads from single-cell RNA-sequencing of peripheral blood of five TET2 mutation carriers as well as three non-carrier family members. Single-cells were captured into 10x barcoded gel beads and RNA-sequencing library preparation was done using Chromium Single Cell 3' v2 chemistry (10x Genomics, Pleasanton, CA, USA). Sequencing was performed as recommended with 98bp length of read 2 using HiSeq4000 sequencer.

  Dataset EGAD00001004778

• A spatiotemporal organ-wide gene expression and cell atlas of the developing human heart

  Dataset includes 2 scRNA-seq samples from a 6.5-7 post-conception weeks human embryonic heart and 19 samples from 4.5-9 post-conception weeks human embryonic hearts analyzed with the Spatial Transcriptomics method. H&E stains can be sent if requested.

  Dataset EGAD00001005468

• Epigenomic analysis of human dopaminergic neuron differentiation reveals LBX1, NHLH1 and NR2F1/2 as necessary for lineage specification

  Sample information: The 56 samples produced in this project come from the human iPSC line GM17602 (Coriell) where a tyrosine hydroxylase-T2A-mCherry reporter was inserted. A combination of epigenetic analysis (ATAC/ChIP) along transcriptomics.

  Dataset EGAD00001009288

• Bulk RNAseq data of scrambled and siRNA-mediated knock-down of the minor spliceosome snRNA U6atac

  Bulk RNAseq data of scrambled and siRNA-mediated knock-down of the minor spliceosome snRNA U6atac in androgen-sensitive LNCaP cells (L), androgen-insensitive C4-2 (C) and 22Rv1 (R) cells and in patient derived neuroendocrine organoids PM154 (P).

  Dataset EGAD00001008034

• Bam files from whole exome sequencing (WES)from multiple laser microdissected regions from tumor and paired biopsies from metastatic lesions.

  In this study we characterized genomic alterations in three bladder cancer patients with metastatic disease courses. Multiple regions were procured by laser microdissection or punctures from primary tumor, lymph node metastases and from distant metastases. Data provided here consist of 35 Bam files for WES (32 Tumors and 2 blood, 1 adjacent normal)

  Dataset EGAD00001002772

• A Single Complex Agpat2 Allele In A Patient With Partial Lipodystrophy data

  The dataset contains data from a single patient sample with partial lipodystrophy. The data is supplied in the form of 2 files. , a BAM file containing the (raw) sequencing data and a VCF file containing the called variants. The data is limited to a region consisting of the AGPAT2 gene on chromosome 9 and 1MB on both sides.

  Dataset EGAD00001004314

• single-cell transcriptomics data from immune cells

  Smart-seq2 protocol was used to perform single cell RNA-sequencing on 465 immune cells. The immune cells analysed include 215 HLA-DQ2: gluten-(DQ2.5-glia-α1, -α2, -ω1, and -ω2) tetramer-sorted T cells, 247 transglutaminase 2 (TG2)-positive plasma cells from intestinal biopsy or peripheral blood from celiac disease patients, and 3 unassigned cells in 3 batches.

  Dataset EGAD00001004081

• RNA sequencing of tumor samples from patients with BPLL

  RNA-Seq was performed on 12 samples of sorted CD19+ tumor cells. RNA-Seq libraries were prepared using the SureSelect Automated Strand Specific RNA Library Preparation Kit as per manufacturer’s instructions (Agilent technologies) and subjected to paired-end (2 x 100 bp) sequencing on HiSeq2000 (Illumina). The files are in FASTQ format.

  Dataset EGAD00001004412

• Combined DNA Methylation and Genotyping via scTAMARA-seq (DNA)

  This dataset features single-cell DNA methylation and nuclear genotyping data obtained using the scTAMARA-seq protocol, a combination of SDR-seq and scTAM-seq. The targeted panel, 200 DNA methylation (a subset of the orginal 448 CpG targets) and 167 genotyping targets, were applied to a CD34+ enriched bone marrow sample from patient X.1. The data was generated on the Mission Bio Tapestri platform.

  Dataset EGAD00001015496

• RNA expression profiling of melanoma patient-derived xenograft

  Patient-derived xenografts (n=96) were derived from metastatic melanoma patients. RNA expression profiling will be preformed to study 1. HLA-typing and 2. the effect of the tumour microenvironment on tumour growth This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Dataset EGAD00001002230

• Ovarian cancer sample size analysis

  The dataset contains exome sequencing fastq from 5 ovarian cancer patients, paired with tumor normal blood samples. Three tumor samples were sequenced from each patient: a biopsy sample ("-1" suffix in the file name), a local sample (multiple regions around the biopsy pooled together, with the "-2" suffix in the file name), and a global sample (multiple regions from the tumor pooled together, with a "-3" suffix in the file name).

  Dataset EGAD00001005947

• Next Generation Sequencing Characterization of Tregs in Human Peripheral Blood during Autoimmunity

  Tregs were sorted as CD4+CD25+CD127- cells from peripheral blood of 14 healthy individuals, 8 patients with systemic lupus erythematosus, 9 patients with rheumatoid arthritis, and 11 patients with multiple sclerosis. RNA was extracted and polyA libraries were prepared using the Illumina Truseq sample preparation kit v.2. Single-end sequencing was performed on NextSeq500.

  Dataset EGAD00001006193

• Re-Evaluation of Systemic Early Neuromuscular Blockade

  This study of the ROSE trial data explored two distinct molecular subtypes of ARDS (Acute Respiratory Distress Syndrome) to better understand the disease's complexity and potential for personalized treatment. Previous studies had identified different inflammatory profiles in ARDS patients, with this research addressing three key questions: Can these molecular subtypes be consistently identified in a more severe group of ARDS patients? Do these subtypes respond differently to neuromuscular blockade treatment? What specific biological processes differentiate these inflammatory profiles? Advanced transcriptomic and protein analyses examined blood samples from ARDS patients. Analysis of these data revealed two main molecular phenotypes: Hypoinflammatory phenotype (60.4% of patients) Hyperinflammatory phenotype (39.6% of patients) Key findings demonstrated that the hyperinflammatory subtype was associated with:Significantly higher mortality rates relative to hypoinflammatory (61.6% vs. 30.3%)Significantly higher mortality rates relative to hypoinflammatory (61.6% vs. 30.3%)Distinct gene expression patterns related to immune responseUnique changes in genes associated with tissue remodeling and cellular processes Notably, the neuromuscular blockade treatment showed no difference in effects across these subtypes. Complex relationships emerged between gene expression and protein levels, with some genes closely matching their protein counterparts and others displaying more variable connections. The study concludes that these molecular phenotypes possess distinct clinical, protein, and genetic characteristics, suggesting potential for more precise, personalized approaches to ARDS treatment in the future.

  Study phs003929

• WES data (cfTrack study) from NSCLC patients and OC patients

  We also collected samples from 8 NSCLC patients and 4 ovarian cancer patients and. For all 8 NSCLC patients, a tumor biopsy sample, a WBC sample, and three plasma samples were collected. For all 4 ovarian cancer patients, a WBC sample and two serum samples were collected. We collected tumor tissue sample from one ovarian cancer patient (OV4). The cfDNA was extracted from their plasma samples using the QIAamp circulating nucleic acid kit from QIAGEN (Germantown, MD). For serum cfDNA, ampure XP beads size selection was further performed to eliminate gDNA contamination. In brief, 0.5 volume of beads were first added to the cfDNA samples. After incubation, the supernatant was transferred to a new tube and an additional 2.0 volume of beads were added. After 80% ethanol wash, cfDNA was eluted from the beads. FA assays (Agilent Technologies) were performed to rule out the contamination of gDNA in the size selected samples. The cfDNA WES library of all patients and the genomic DNA WES library of the 4 ovarian cancer patients were constructed with the SureSelect XT HS kit from Agilent Technologies (Santa Clara, CA) according to the manufacturer’s protocol. In brief, 10ng of cfDNA was used as input material. After end repair/dA-tailing of cfDNA, the adaptor was ligated. The ligation product was purified with Ampure XP beads (Beckman-Coulter, Atlanta, GA) and the adaptor-ligated library was amplified with index primer in 10-cycle PCR. The amplified library was purified again with Ampure XP beads, and the amount of amplified DNA was measured using the Qubit 1xdsDNA HS assay kit (ThermoFisher, Waltham, MA). 700-1000 ng of DNA sample was hybridized to the capture library and pulled down by streptavidin-coated beads. After washing the beads, the DNA library captured on the beads was re-amplified with 10-cycle PCR. The final libraries were purified by Ampure XP beads. The library concentration was measured by Qubit, and the quality was further examined with Agilent Bioanalyzer before the final step of 2x150bp paired-end sequencing at an average coverage of 200. Whole-exome capture libraries of genomic DNA from the 8 NSCLC patients were constructed via Roche SeqCap EZ Exome V6 (Roche). Enriched exome libraries were sequenced on the Illumina HiSeq 3000 platform (Illumina) to generate 2x100bp paired-end reads at an average coverage of 200.

  Dataset EGAD00001008454

• NHLBI GO-ESP: Family Studies (Familial Atrial Fibrillation)

  The NHLBI "Grand Opportunity" Exome Sequencing Project (GO-ESP), a signature project of the NHLBI Recovery Act investment, was designed to identify genetic variants in coding regions (exons) of the human genome (the "exome") that are associated with heart, lung and blood diseases. These and related diseases that are of high impact to public health and individuals from diverse racial and ethnic groups will be studied. These data may help researchers understand the causes of disease, contributing to better ways to prevent, diagnose, and treat diseases, as well as determine whether to tailor prevention and treatments to specific populations. This could lead to more effective treatments and reduce the likelihood of side effects. GO-ESP is comprised of five collaborative components: 3 cohort consortia - HeartGO, LungGO, and WHISP - and 2 sequencing centers - BroadGO and SeattleGO. Large epidemiological studies have demonstrated a significant heritable component in atrial fibrillation (AF), especially the Lone forms, suggesting a monogenic syndrome. Although substantial genetic contribution has been made to the etiology of AF, the specific genes have not yet been identified. The familial form of this disease remains poorly characterized and largely undetermined. Here we seek to identify, characterize and determine the natural course of AF in our clinical practice. We identified four large multi-generation families (FAF 1-4). In FAF 1-2, most family members have symptomatic paroxysmal Atrial Fibrillation (AF) and were adequately treated with a combination of rate and rhythm therapies. By contrast, the AF substrate in FAF 3 and 4 was resistant to anti-arrhythmic drugs and ablation therapies.

  Study phs000362

• NHLBI GO-ESP: Family Studies (Thoracic aortic aneurysms leading to acute aortic dissections)

  The NHLBI "Grand Opportunity" Exome Sequencing Project (GO-ESP), a signature project of the NHLBI Recovery Act investment, was designed to identify genetic variants in coding regions (exons) of the human genome (the "exome") that are associated with heart, lung and blood diseases. These and related diseases that are of high impact to public health and individuals from diverse racial and ethnic groups will be studied. These data may help researchers understand the causes of disease, contributing to better ways to prevent, diagnose, and treat diseases, as well as determine whether to tailor prevention and treatments to specific populations. This could lead to more effective treatments and reduce the likelihood of side effects. GO-ESP is comprised of five collaborative components: 3 cohort consortia - HeartGO, LungGO, and WHISP - and 2 sequencing centers - BroadGO and SeattleGO. Acute aortic dissections are a common cause of premature death in the United States, ranking as high as the 15th leading cause of death. The goal of the Familial Thoracic Aortic Aneurysm and Dissection (TAAD) study at the University of Texas Health Science Center at Houston is to identify the genes causing thoracic aortic disease, and prevent premature deaths due to aortic dissections by identifying individuals who are genetically predisposed to the disease and initiating medical and surgical therapies to prevent dissections. In this study ("NHLBI GO-ESP Family Studies: Aortic Disease"), we have selected a series of families from the TAAD study, and are performing exome sequencing of 2 to 3 individuals per family.

  Study phs000347

• Follow-up of Ovarian Cancer Genetic Association and Interaction Studies (FOCI)

  (Excerpted/paraphrased from original grant application): FOCI seeks to expand our understanding of epithelial ovarian cancer through a coordinated and comprehensive approach. Project 1 will focus on discovery, expansion, and replication. By pooling GWAS, we expect to identify new associations and achieve independent replication, explore whether there are risk variants specific for histologic subtypes, and evaluate structural polymorphisms - copy number variants - as risk factors. Finally, Project 1 will leverage the GWAS data to correlate DNA variants with a new endpoint - survival. Project 2 will focus on biological studies designed to help inform interpretation of findings from Project 1. This will include efforts to identify the functional consequences of variants and improve understanding of biological mechanisms. Project 3 will include epidemiologic studies of gene by gene interaction, gene by environment interaction, and development of risk prediction models. The collective effort builds upon the strengths and history of collaboration inherent in the Ovarian Cancer Association Consortium (OCAC), a multidisciplinary group comprised of epidemiologists, genetic epidemiologists, statistical geneticists, molecular and cell biologists and clinicians that was formed in 2005. The FOCI Cohort is utilized in the following dbGaP sub-studies. To view genotypes, other molecular data, and derived variables collected in these sub-studies, please click on the following sub-studies below or in the "Sub-studies" box located on the right hand side of this top-level study page phs001133 FOCI Cohort. phs001131 Affymetrix Exome Chip phs001132 GWAS Meta Analysis phs001142 Mayo Omni Express phs001150 Mayo 2 5M

  Study phs001133

• Melbourne Collaborative Cohort Study DNA Methylation Studies

  This dataset contains raw Illumina 450K blood DNA methylation data from a subset of participants in the Melbourne Cohort Study (MCCS), a prospective study of 41,513 healthy adult volunteers (24,469 women) aged between 27 and 76 years when recruited between 1990 and 1994. Nested case-control studies: DNA methylation data were generated as part of cancer case-control studies nested in the MCCS. Participants were cancer-free at blood draw; blood samples were taken at baseline (1990-1994) for 97% of participants; and for 3% of participants at the second wave of follow-up (2003-2007). Eight separate studies were conducted of breast, prostate, colorectal, lung, kidney, urothelial and gastric cancer and B-cell lymphoma, for a total of > 3,500 cancer cases. Controls were individually matched to cases on age, sex, and country of birth using incidence density sampling. Additional matching on smoking history was made for the study of lung cancer. Longitudinal study: For a subset of 1,100 participants with baseline DNA methylation measures (from dried blood spots) who were selected as controls in the nested case-control studies, repeated methylation measures were made using wave 2 follow-up samples (also from dried blood spots) to study longitudinal DNA methylation changes. Project aims: 1. Nested case-control studies: To assess prospective associations between peripheral blood DNA methylation and risk of eight cancer types (breast, prostate, colorectal, lung, kidney, urothelial cell and gastric cancer, and mature B-cell neoplasms). 2. Longitudinal study: To assess associations between lifestyle changes and changes in peripheral blood DNA methylation.

  Study phs003213

• Efficacy of nivolumab in pediatric cancers with high mutation burden and mismatch-repair deficiency

  Purpose: Checkpoint-inhibitors have limited efficacy for children with unselected solid and brain tumors. We report the first prospective pediatric trial (NCT02992964) using nivolumab exclusively for refractory non-hematological cancers harboring tumor mutation burden (TMB) ≥5 mutations/megabase (mut/Mb) and/or mismatch-repair deficiency (MMRD). Patients and methods: Twenty patients were screened, and ten ultimately included in the response cohort of whom nine had TMB >10mut/Mb (three initially eligible based on MMRD) and one patient had TMB between 5-10 mut/Mb. Results: Delayed immune responses contributed to best overall response of 50%, improving on initial objective responses (20%) and leading to 2-year overall survival (OS) of 50% (95% CI; 27, 93). Four children, including three with refractory malignant gliomas are in complete remission at a median follow-up of 37-months (range: 32.4-60), culminating in 2-year OS of 43% (95% CI; 18.2, 100). Biomarker analyses confirmed benefit in children with germline MMRD, microsatellite instability, higher activated and lower regulatory circulating T-cells. Stochastic mutation accumulation driven by underlying germline MMRD impacted the tumor microenvironment, contributing to delayed responses. No benefit was observed in the single patient with a MMR-proficient tumour and TMB 7.4 mut/Mb. Conclusions: Nivolumab resulted in durable responses and prolonged survival for the first time in a pediatric trial of refractory hypermutated cancers including malignant gliomas. Novel biomarkers identified here need to be translated rapidly to clinical care to identify children who can benefit from checkpoint-inhibitors, including for upfront management of their cancers.

  Study EGAS00001007393

• Genome-Wide Association of Native and Post Aspirin Platelet Function Phenotypes

  The goal of this study was to identify genetic variants in a genome-wide association study (GWAS) that are associated with previously obtained platelet function phenotypes measured in each individual under baseline conditions and following 2 weeks of low dose aspirin (ASA). During this study we performed a high density 1 million-SNP genome scan on subjects from GeneSTAR (representing 800 2-generational families with a family history of premature coronary artery disease, 60% white and 40% African American, N=3232). We identified genomic loci associated with quantitative platelet phenotypes prioritized for their biological interest, determined associations between genomic loci and baseline platelet phenotypes (primary phenotypes are platelet aggregation in platelet rich plasma induced by collagen, adenosine diphosphate (ADP), arachidonic acid (AA), and epinephrine (Epi), determined associations between genomic loci and post-ASA platelet phenotypes, ie, measures of ASA "resistance" (primary phenotypes are as above, plus urinary levels of the prostaglandin metabolite, 11-dehydro-thromboxane B2 ), and compared peaks of association between genomic loci and three common baseline platelet phenotypes (collagen-, epinephrine-, and ADP-induced aggregation in platelet rich plasma) with associations found for these same phenotypes in the Framingham Heart Study. We also determined whether any significant genotype-phenotype associations in the 1 million SNP genome scan could be localized to any specific genes or potential genes of interest using publicly available databases and further examined whether candidate genes previously associated with a specific platelet phenotype are located in a genomic region of interest as determined from the SNP genome scan. We conducted replications of our findings, and are presently involved in larger scale meta-analysis of findings for pre-aspirin and post-aspirin associations. The study population is constituted of full siblings (SIBS) (ages 35-78 years) identified from The Johns Hopkins Sibling Study, now called GeneSTAR, the spouses of the SIBS, and their adult offspring (>21 years of age). They include 3200 individuals from approximately 300 African American and 500 white extended families. "Spouse" refers to the other parent of any SIB offspring, independent of marital status. Sibship sizes among families range from 1 to 16 (excluding index cases). On average, each SIB has 2 potentially eligible offspring. A family for this study is defined by all of the full sibships and the total numbers of offspring that come from all SIBS, rather than just the nuclear family.

  Study phs000375

• Heart Failure Network: Functional Impact of GLP-1 for Heart Failure Treatment (HFN FIGHT-BioLINCC)

  Objectives To test whether therapy with a GLP-1 agonist improves clinical stability following hospitalization for acute heart failure. Background Heart failure was the leading cause of hospitalization in the United States with more than 4 million admissions per year from 2003–2009. Abnormal cardiac metabolism contributes to the pathophysiology of advanced heart failure with reduced left ventricular ejection fraction (LVEF). As heart failure progresses, these abnormalities become more pronounced and are observed in both patients with and without type 2 diabetes. At this time of this study, there was no heart failure therapy that targeted these metabolic abnormalities; however, in earlier clinical studies, glucagon-like peptide 1 (GLP-1) agonists showed cardioprotective effects in patients with advanced heart failure, irrespective of type 2 diabetes status. Glucagon-like peptide 1 is an endogenous incretin hormone that improves insulin sensitivity with minimal risk of hypoglycemia. This study was created to determine if use of GLP-1 agonists improved clinical stability in recently hospitalized patients with acute heart failure and reduced LVEF. Participants There were 300 participants. Design Participants were identified by hospital admission records and were enrolled during either the last 24 hours of his or her hospitalization for heart failure or the 2-week interval after the hospitalization. Baseline evaluations were conducted, which included echocardiographic measures, the 6-minute walk test, the Kansas City Cardiomyopathy Questionnaire (KCCQ), and blood tests. After the baseline evaluation, patients were randomized in a 1:1 ratio to receive either the GLP-1 agonist liraglutide or placebo as a daily subcutaneous injection. The protocol involved titration of study drug dosage as tolerated every 14 days from 0.6 mg/d to 1.2 mg/d to 1.8 mg/d during the first 30 days of the trial (as tolerated). Follow-up testing was performed at 30-, 90-, and 180-day study visits. The primary end point was a global rank score in which all participants, regardless of treatment assignment, were ranked across 3 hierarchical tiers: time to death, time to rehospitalization for heart failure, and time-averaged proportional change in N-terminal pro-B-type natriuretic peptide (NT-proBNP) level from baseline to 180 days. Conclusions The GLP-1 agonist liraglutide did not improve post-hospitalization clinical stability in patients with advanced heart failure and reduced LVEF. There was no significant between-group difference in the global rank scores and furthermore, there were no significant differences detected in any of the secondary endpoints.

  Study phs003542

• FFPE cohort with RNA-seq data of tumor samples

  This dataset contains RNA-seq raw data in fastq format from 14 tumor samples. The samples are from primary tumors or metastasis and represent various cancer entities. The samples are formalin-fixed paraffin-embedded (FFPE) treated. For target enrichment SureSelect XT Human All Exon V6 was used. The libraries were sequenced in paired-end mode (2 x 50 nt) on a NovaSeq6000 S2 flow cell.

  Dataset EGAD00001006781

• Prospective cohort patients with Multiple sclerosis and controls

  The sys4MS cohort comprises 350 patients with Multiple Sclerosis (MS) and 9 controls, with 2 years of follow-up. Baseline data includes demographics, clinical scales, disease duration and subtype and use of disease-modifying drugs, brain MRI (volumetry and lesion load), retinal thickness by OCT, genomics (GWAS), cytomics, and phosphoproteomics. Data at the end of follow-up includes clinical scales, brain MRI and OCT.

  Dataset EGAD00010002505

• Dataset for Fragle Software Development and Evaluation

  Fragle is a deep learning based two stage model that quantifies ctDNA from blood plasma derived cfDNA bam files. Fragle was developed using some previously published datasets and some newly generated data. Fragle was evaluated using some validation cohorts and some unseen cohorts. Some of these cohorts are newly created consisting of total 365 low pass (2-3X) whole genome sequencing bam files mapped to hg19/GRCh37. This dataset contains these newly generated bam files.

  Dataset EGAD50000000167

• iPSC and iPSC derived pericytes

  Bulk RNA sequencing of iPSCs and iPSC derived pericytes from three cell lines MNZTASi019-A, MNZTASi021-A and MNZTASi022-A. Data includes one iPSC data set per cell line and iPSC derived pericyte differentiations per cell line (3 differentiations from MNZTASi019-A and MNZTASi021-A, 2 from MNZTASi022-A). RNA-seq data was generated using an Illumina Stranded mRNA 150bp paired-end library preparation.

  Dataset EGAD50000000255

• CITE-seq AdaptNK

  CITEseq was performed as outlined in Biolegend ‘TotalSeqTM-A Antibodies and Cell Hashing with 10x Single Cell 3' Reagent Kit v3 3.1 Protocol’ with minor modifications, using Biolegend oligo-conjugated antibodies and streptavidin TotalSeq reagents. Briefly, ADAPT-NK cells were stained with CD56-biotin mAb (Miltenyi, clone REA196), followed by TotalSeq antibodies and streptavidin-PE and Live/Dead Aqua (Invitrogen). Cells were subsequently sorted for viable CD56+ cells by flow cytometry.

  Dataset EGAD50000000329

• PBMC scRNA-seq data using 10X Genomics platform

  Matrices of counts from single-cell RNA-seq data and single-cell CITE-seq data collected from 16 patients enrolled in GO30103 trial, and the cell level annotation. Specifically, PBMCs at C1D1, C1D15 (2 weeks after treatment), C2D1 (3 weeks after treatment) and C4D1 (9 weeks after treatment) were collected and subject to 10x Genomics protocol. Associated metadata also included.

  Dataset EGAD50000000370

• BCR sequences and metadata for cultured single B-cell clones from blood

  The dataset contains VDJ sequences in FASTA format, the same sequences run through IMGT/HighV-QUEST (tsv file) and accompanying metadata (csv file) including antigen specificity (transglutaminase 2-specific or other). The data was generated from cultured single B-cell clones from the peripheral blood of four untreated celiac disease patients. Sequences were obtained by a nested RT-PCR approach targeting the immunoglobulin chains followed by Sanger sequencing.

  Dataset EGAD50000000343

• Ischemia Reperfusion Responses in Human Lung Transplants at the Single Cell Resolution

  Ischemia reperfusion is an unavoidable step of organ transplantation. Development of therapeutics for lung injury during transplantation has proved challenging; understanding lung injury from human data at the single cell resolution is required to accelerate the development of therapeutics. Donor lung biopsies from six human lung transplant cases were collected at the end of cold preservation and 2-hour reperfusion and underwent single cell RNA sequencing.

  Dataset EGAD50000000704

• Whole Genome DNA Methylation

  Whole Genome Bisulfite Sequencing on normal primary human uveal melanocytes. WGBS libraries were prepared using the Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences 30024), the EZ DNA Methylation-Gold Kit (Zymo D5005), and DNA Clean & Concentrator-5 (Zymo D4013), following the instruction manual Accel-NGS Methyl-Seq DNA Library (Revision 160510). Paired-end (2 x 150 bp) libraries were sequenced on a DNBSEQ-T7 instrument (MGI) after library conversion.

  Dataset EGAD50000000766

• RNA sequencing of Ewing sarcoma and CIC-DUX4 sarcoma

  RNA sequencing of a collection of 6 Ewing sarcoma and 3 CIC-DUX4 sarcoma tumoroids plus 3 matched patient tumors. Tumoroids were established from digested patient tumor material as 3D culture in Matrigel. After 2-3 month of growth, RNA was isolated from individual tumoroid models using the RNeasy Kit (Qiagen) and used for whole exome sequencing. RNA from corresponding patient tumors was tested in parallel, if available.

  Dataset EGAD50000000557

• Anti-MPO BCR sequences described in 'Anti-myeloperoxidase IgM B cells in anti-neutrophil cytoplasmic antibody-associated vasculitis'

  FASTA files from quality-checked Sanger Sequencing results from BCR-specific PCR products. B cells from 4 different MPO+ AAV patients were single cell sorted and processed to sequence the specific BCR, resulting in 51, 175, 12 and 3 heavy chain BCR sequences for AAV1, 2, 3, and 5 respectively. Sequence names indicate patient ID and isotype (IgG, IgM or IgA).

  Dataset EGAD50000001112

• Whole Genome DNA Methylation MPI

  Whole Genome Bisulfite Sequencing on normal primary human uveal melanocytes. WGBS libraries were prepared using the Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences, Catalog No. 30024), the EZ DNA Methylation-Gold Kit (Zymo, D5005) and DNA Clean & Concentrator-5 (Zymo, D4013), following the instruction manual Accel-NGS® Methyl-Seq DNA Library (Revision 160510). Paired-end libraries (2 × 150 bp) were sequenced on a NovaSeq 6000 instrument.

  Dataset EGAD50000001139

• Single-cell Transcriptome Analysis of Plasma Cells Across the Disease Spectrum of Multiple Myeloma

  This dataset includes FastQ files of single-cell RNA sequencing data of 5' GEX and VDJ libraries from CD138+ plasma cells enriched from 72 bone marrow aspirates from patients diagnosed with a monoclonal gammopathy from the multiple myeloma spectrum, including MGUS (n=13), SMM (n = 22), NDMM (n = 17), RRMM (n = 15) and PCL (n = 2); and 3 controls.

  Dataset EGAD50000001179

• DNA Methylation Profiles of T2D and Control Subjects from the GCAT Cohort Using EPIC v2

  This dataset contains DNA methylation data from 400 individuals (200 Type 2 Diabetes cases and 200 controls) from the GCAT (Genomes for Life) cohort. The methylation profiling was performed using the Illumina Infinium MethylationEPIC v2.0 BeadChip, which offers comprehensive coverage of over 850,000 CpG sites. Data are provided in IDAT file format, enabling raw signal-level analysis and downstream processing.

  Dataset EGAD00010002740

• Low-input RNA-seq libraries from FFPE samples using TaKaRa SMARTer kit

  Using the TaKaRa SMARTer Stranded Total RNA-Seq Kit v2, RNA-seq libraries were generated from 5 ng of RNA extracted from FFPE tissue. A low-input workflow was applied with 5 PCR cycles for the first amplification and 16 for the second. Library quality was assessed by Bioanalyzer and Qubit, and libraries were sequenced (2×150 bp) on the Illumina NextSeq 550 platform.

  Dataset EGAD50000001552

• scRNAseq of endothelial cells from human iPSC-derived kidney organoids transplanted in the coelomic cavity of chicken embryos compared to untransplanted controls

  This dataset includes scRNA-seq fastq files and Seurat counts and metadata for 6 samples of endothelial cells enriched from hiPSC-derived kidney organoids cultured in vitro or transplanted in chicken embryos. Samples were obtained at 2 timepoints: d7+13 (1 day after transplantation) and day 7+20 (8 days after transplantation).

  Dataset EGAD50000001555

• Immunoglobulin Heavy-Chain locus in Multiple Sclerosis (n=4)

  Peripheral-blood or monocyte DNA from two healthy donors and two individuals with multiple sclerosis were sequenced on a PromethION-2 Solo (P2 Solo) instrument using R10.4.1 flow-cells and the Ultra-Long DNA Sequencing Kit (SQK-ULK114). For each participant we provide FASTQ reads (on-target), and haplotype-resolved assemblies of the complete IGH locus (~1.3 Mb) in FASTA format.

  Dataset EGAD50000001517

• Chromatin segmentation of myometrium and UL subclasses

  Histone modification ChIP-seq for chromatin state annotations of myometrium and UL subclasses. Altogether 5 analyses and 210 runs. Includes fastq files; both ChIP and Input for each sample. Some Inputs are used for multiple ChIP experiments. ChIP-seq alignment files for trimmed, mapping q20 and nonredundant reads; both ChIP and Input for each sample. Software: Trim Galore v0.6.7; Bowtie 2 v2.5.0; samtools v1.6

  Dataset EGAD50000001443

• WGS data of pediatric T-ALL acute lymphoblastic leukemia (set1)

  The dataset includes FASTQ and BAM files from diagnostic and matched remission (control) samples of one T-ALL patient (ALLT-317). Relapsed (BM ALLT-317L and Tonsil ALLT-3107L) sample files are in dataset set2 of this submission. Sequencing library was made using PCR free-based WGS library preparation (PCR-), using TruSeq DNA PCRfree library preparation kit v1 (PE150). Both diagnostic (60x) and remission (30x) samples were sequenced using HiSeq X.

  Dataset EGAD50000002013