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• Single cell ATAC sequencing

  Paired-end fastq files of 22 AML and 2 normal bone marrow samples were generated using 10x Genomics single cell ATAC sequencing following manufacturer's protocol (CG000168 User Guide RevB) for chemistry version 1.0 and targeting 10000 nuclei per sample. Libraries were sequenced using Illumina HiSeq4000 using recommended cycling parameters.

  Dataset EGAD00001007675

• CGH Array

  DNA samples were extracted from peripheral blood lymphocytes using commercially available kit (Puregene Core Kit A, Qiagen) according to manufacturer's protocol. Agilent SurePrint G3 Human CGH Microarray 180K platform was used for screening of copy number aberrations (CNAs) using array-CGH protocol recommended by manufacturer (Agilent Technologies), data mining and interpretation of array-CGH results was performed in same manner as in our previously published results.

  Dataset EGAD00001007743

• Feb2020 interim Genes and Health (28k) GSA imputed genotyped data

  Genotyped data for 28,022 British individuals with South Asian ancestry from the Genes and Health cohort (Feb2020), which were imputed with the GenomeAsia pilot reference panel.

  Dataset EGAD00001007815

• CNV detection in targeted NGS panel data

  We present targeted NGS panel data from 170 samples that were processed using the TruSightTM Cancer (TSC) panel (Illumina, San Diego, CA, USA), which targets 94 genes and 284 SNPs associated with a predisposition towards cancer. The samples are enriched for CNVs in the genes of interest. All CNVs have previously been assessed with MLPA and can therefore be considered as confirmed.

  Dataset EGAD00001003400

• Whole-exome sequences of ovarian clear cell carcinomas and paired normal DNA

  Whole-exome sequencing dataset for the Australian Ovarian Cancer Study (AOCS) and The Jikei University School of Medicine (JIKEI) ovarian clear cell carcinoma (OCCC) clinical outliers project, representing 10 donors. Consists of 20 fastq files: one normal and one tumour from each patient.

  Dataset EGAD00001006004

• analysis of the off target effect after Prime editing in IPSC line KCNQ2 R201C. Comparison of parental KCNQ2 R201C with two corrected clonal lines.

  Short read whole genome sequencing analysis of the off target effect after Prime editing in IPSC line KCNQ2 R201C. Comparison of parental KCNQ2 R201C with two corrected clonal lines (3samples in total). Dataset contains CRAM files and VCF files for the respective samples.

  Dataset EGAD00001010904

• NIHR BioResource Rare Diseases WGS project - Steroid Resistant Nephrotic Syndrome (SRNS) Rare Disease domain

  Short read whole genome sequencing (WGS) CRAM files for the NIHR BioResource Rare Diseases WGS project – Participants from the Steroid Resistant Nephrotic Syndrome (SRNS) Rare Disease domain

  Dataset EGAD00001004518

• Low-depth whole genome sequencing across multiple isolated populations

  Isolated populations have unique population genetics characteristics that can help boost power in genetic association studies for complex traits. Leveraging these advantageous characteristics requires an in-depth understanding of parameters that have shaped sequence variation in isolates. This study performs a comprehensive investigation of these parameters using low-depth whole genome sequencing (WGS) across multiple isolates.

  Dataset EGAD00001002014

• Integrated analysis of whole genome and RNA sequencing in 22 HBV-associated HCCs

  RIKEN collection WGS and RNA-seq reads for 66 HBV-associated HCC and matched blood or liver samples from 22 donors.

  Dataset EGAD00001001035

• 10x genomics RNAseq of an isogenic human iPSC model of SMA

  10x genomics single-cell RNAseq of an isogenic human iPSC model for SMA and control. The transcriptomic analysis was performed at 3 timepoints, day 4, day 20 and day 40. The analysis of this dataset was reported in the manuscript "An isogenic human iPSC model unravels neurodevelopmental abnormalities in SMA" from Grass et al.:

  Dataset EGAD00001011259

• Sequencing data for ICGC Oesophageal Adenocarcinoma tissue samples - barretts_1

  Samples from Ross Innes et. al 2015 - doi:10.1038/ng.3357

  Dataset EGAD00001001394

• Whole transcriptome sequencing of 38 follicular lymphoma tumours.

  This data set includes RNAseq from 38 follicular lymphoma tumours. All tumours were fresh frozen. Libraries were constructed by enriching for poly-A transcripts and sequenced as 75bp paired end reads on an Illumina HiSeq 2500 instrument.

  Dataset EGAD00001009650

• Single cell BCR sequencing

  Paired-end fastq files of 22 AML and 2 normal bone marrow samples were generated using 10x Genomics single cell BCR sequencing following manufacturer's protocol (CG000086 User Guide RevG) for chemistry version 1.0 and targeting 10000 cells per sample. Libraries were sequenced using Illumina NovaSeq 6000 using recommended cycling parameters.

  Dataset EGAD00001007673

• Single cell TCR sequencing

  Paired-end fastq files of 22 AML and 2 normal bone marrow samples were generated using 10x Genomics single cell TCR sequencing following manufacturer's protocol (CG000086 User Guide RevG) for chemistry version 1.0 and targeting 10000 cells per sample. Libraries were sequenced using Illumina NovaSeq 6000 using recommended cycling parameters.

  Dataset EGAD00001007674

• cfMeDIP data for 30 CPC-GENE samples

  We analyzed the cell free DNA methylomes using 30 plasma samples from patients with localized prostate cancer in the CPC-GENE project. Methylation was profiled using the methylated DNA immunoprecipitation coupled to next generation sequencing (MeDIP) technology.

  Dataset EGAD00001007972

• Single Cell RNA sequencing of Organoids from TSC2+/- patient IPSCs in H- and L-medium

  This dataset contains single cell RNA sequencing data from Organoids grown in high nutrient (H) and low nutrient (L) medium. Organoids were grown for 110 days. Organoids were grown from a patient IPS cell line with a heterozygous mutation in TSC2 (Patient 1 TSC2+/- iPSCs) and an isogenic control cell line (TSC2+/+).

  Dataset EGAD00001006332

• Dataset for head_and_neck_cancer-WHOLE_GENOME

  Rare cancer sequencing data of 56 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008879

• SMARTer bulk RNA sequencing for highly purified CD271+ BMSCs from NBM and AML

  bulk RNAseq was conducted on highly purified CD45 - CD71 - CD235a - CD31 - CD271 + BMSCs isolated from a cohort of newly diagnosed 62 AML patients, uniformly treated within an intensive chemotherapy clinical trial and selected to represent the mutational landscape of AML

  Dataset EGAD00001011056

• Dataset for liposarcoma-WHOLE_GENOME

  Rare cancer sequencing data of 48 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008888

• Dataset for NSCLC-WHOLE_GENOME

  Rare cancer sequencing data of 34 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008894

• Cystic Fibrosis Varsity Project Multi-omics data

  This Dataset contains RNA-Seq, H3K27Ac ChIP-Seq, and ATAC-Seq data for 13 cystic fibrosis (CF) patients and 8 healthy volunteers (HV).

  Dataset EGAD00001009062

• scRNA-seq from brain metastasis micorenvironment and cerebrospinal fluid

  A total of 9 brain metastasis were sequenced. For 6/9 a matched cerebrospinal fluid sample, prior to surgery and in two cases after surgery (+1 month from surgery) and after treatment (+3 month) were collected. Single-cell gene expression was produced using the Chromium Single Cell 5’ Library and sequenced on an Illumina NovaSeq 6000.

  Dataset EGAD00001006452

• Sequencing data for ICGC Oesophageal Adenocarcinoma tissue samples - 100

  Samples from the "100" project that are in the ICGC PanCancer project.

  Dataset EGAD00001001071

• NIHR BioResource Rare Diseases WGS project - Bleeding, Thrombotic and Platelet Disorders (BPD) Rare Disease domain

  Short read whole genome sequencing (WGS) CRAM files for the NIHR BioResource Rare Diseases WGS project – Participants from the Bleeding, Thrombotic and Platelet Disorders (BPD) Rare Disease domain

  Dataset EGAD00001004519

• Finding structural variation and functional consequences from the Skin fibroblast at the single-cell level

  In this study, we aimed to identify somatic structural variation of Skin fibroblast at the single-cell level and investigate its direct consequence on the nucleosome occupancy using scNOVA approach. For this purpose, we performed strand-specific single-cell sequencing of skin fibroblast sample from male donor.

  Dataset EGAD00001009307

• Finding structural variation and functional consequences from the primary leukemia cells (CLL) at the single-cell level

  In this study, we aimed to identify somatic structural variation of chronic lymphocytic leukemia (CLL) at the single-cell level and investigate its direct consequence on the nucleosome occupancy using scNOVA approach. For this purpose, we performed strand-specific single-cell sequencing of primary leukemia samples from 63-year-old female patient.

  Dataset EGAD00001006822

• NIHR BioResource Rare Diseases WGS project - Neurological and Developmental Disorders (NDD) Rare Disease domain

  Short read whole genome sequencing (WGS) CRAM files for the NIHR BioResource Rare Diseases WGS project – Participants from the Neurological and Developmental Disorders (NDD) Rare Disease domain

  Dataset EGAD00001004522

• 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

• ESGI - Whole Genome Sequencing of samples from the ORCADES cohort (X10) (2019-08-19)

  Deep whole genome sequencing of sampels from the Orkney Complex Disease Study (ORCADES), each with data on up to 300 quantitative traits and other risk factors associated with cardiovascular, metabolic and other complex diseases. The samples are sequenced using the Illumina HiSeq X Ten system. . This dataset contains all the data available for this study on 2019-08-19.

  Dataset EGAD00001005269

• Dataset on keratinocytic gene expression pattern in Hidradenitis suppurativa

  Human skin samples were obtained from HS patients after informed consent (Ethical vote, University of Würzburg; No. 306/12). Lesional and perilesional were taken and epidermis and dermis separated. Isolated epidermal keratinocytes were further processed for RNA isolation. mRNA was extracted from five pairwise-matched lesional and perilesional epidermal HS pellets and RNA sequencing was performed.

  Dataset EGAD00001008005

• NIHR BioResource Rare Diseases WGS project - Stem cell and Myeloid Disorders (SMD) Rare Disease domain

  Short read whole genome sequencing (WGS) CRAM files for the NIHR BioResource Rare Diseases WGS project – Participants from the Stem cell and Myeloid Disorders (SMD) Rare Disease domain

  Dataset EGAD00001004524

• 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

• NIHR BioResource Rare Diseases WGS project - Multiple Primary Malignant Tumours (MPMT) Rare Disease domain

  Short read whole genome sequencing (WGS) CRAM files for the NIHR BioResource Rare Diseases WGS project – Participants from the Multiple Primary Malignant Tumours (MPMT) Rare Disease domain

  Dataset EGAD00001004521

• 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

• Exome Atlas in HCC tumors

  The atlas provides a comprehensive exploration of genetic and transcriptomic landscapes within HCC, offering insights into key genomic alterations and gene expression patterns. The integration of exome sequencing and RNAseq data enhances our understanding of the molecular complexity underlying HCC, potentially paving the way for targeted therapeutic strategies and biomarker discovery in the context of hepatocellular carcinoma.

  Dataset EGAD00001015342

• Whole-exome sequencing of liver cancer organoids

  Whole-exome sequencing was performed from organoids derived from 10 liver cancer biopsies (7 hepatocellular carcinoma and 3 cholangiocarcinoma), corresponding liver and non-tumoral biopsies. For 3 of the organoids, both early and late passage organoids were sequenced. Whole-exome sequencing was performed using the Agilent Clinical Research Exome capture kit followed by Illumina sequencing. BAM files are provided in this dataset.

  Dataset EGAD00001004205

• Dataset for the study - Detection of cell-free DNA fragmentation and copy number alterations in cerebrospinal fluid from glioma patients

  FASTQ files from sequencing to < 0.4x depth of coverage of thirteen glioma patients. Indexed sequencing libraries were prepared using a commercially available kit (ThruPLEX-Plasma Seq, Rubicon Genomics). Libraries were pooled in equimolar amounts and sequenced on a HiSeq 4000 (Illumina) generating 150-bp paired-end reads.

  Dataset EGAD00001004425

• NIHR BioResource Rare Diseases WGS project - Cerebral Small Vessel Disease (CSVD) Rare Disease domain

  Short read whole genome sequencing (WGS) CRAM files for the NIHR BioResource Rare Diseases WGS project – Participants from the Cerebral Small Vessel Disease (CSVD) Rare Disease domain

  Dataset EGAD00001004513

• MGRB dataset. Samples that were not included in the paper.

  This dataset comprises 1440 whole genome sequenced samples from the Medical Genome Reference Bank. https://sgc.garvan.org.au/initiatives/mgrb The files are provided in cram format, aligned to hs37d5 with decoys, with no further processing applied. The dataset also contains phenotype information for each sample.

  Dataset EGAD00001005095

• NIHR BioResource Rare Diseases WGS project - Leber Hereditary Optic Neuropathy (LHON) Rare Disease domain

  Short read whole genome sequencing (WGS) CRAM files for the NIHR BioResource Rare Diseases WGS project – Participants from the Leber Hereditary Optic Neuropathy (LHON) Rare Disease domain

  Dataset EGAD00001005122

• A Single-Cell Atlas of the Multicellular Ecosystem of Primary and Metastatic Hepatocellular Carcinoma

  Single-cell transcriptomes for 10 hepatocellular carcinoma (HCC) patients from 21 sample of four relevant sites: primary tumor (T), portal vein tumor thrombus (P), metastatic lymph node (L) and non-tumor liver (N). Single cells were sequenced using Chromium Single Cell 3’ Library (10x Genomics).

  Dataset EGAD00001006190

• scTCR-seq from brain metastasis micorenvironment and cerebrospinal fluid

  A total of 9 brain metastasis were sequenced. For 6/9 a matched cerebrospinal fluid sample, prior to surgery and in two cases after surgery (+1 month from surgery) and after treatment (+3 month) were collected. Single-cell T cell receptor clonotypes were produced using the Chromium Single Cell 5’ Library and sequenced on an Illumina NovaSeq 6000.

  Dataset EGAD00001006451

• Finding structural variation and functional consequences from the primary leukemia cells (AML) at the single-cell level

  In this study, we aimed to identify somatic structural variation of acute myeloid leukemia (AML) at the single-cell level and investigate its direct consequence on the nucleosome occupancy using scNOVA approach. For this purpose, we performed strand-specific single-cell sequencing of primary leukemia samples from 32-year-old male donor.

  Dataset EGAD00001006782

• Illumina RNA-Seq paired of 10 different tumor samples from the Master program (H021)

  Fastq files of paired RNA-Seq of 10 different tumor samples, for which Nanopore and Illumina sequencing was compared. Illumina sequencing was carried out with HiSeq4000 or HiSeq X-Ten using the Illumina TruSeq stranded mRNA Kit.

  Dataset EGAD00001008971

• Whole transcriptome sequencing of 78 follicular lyphoma tumours

  This data set includes RNAseq from 77 follicular lymphoma tumours. All tumours were fresh frozen. Libraries were constructed by enriching for poly-A transcripts and sequenced as 75bp paired end reads on an Illumina HiSeq 2500 instrument.

  Dataset EGAD00001010894

• 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

• Liquid biopsy-based minimal residual disease monitoring for early risk stratification and decision-making in advanced non-small cell lung cancer

  Circulating tumor DNA (ctDNA)-based minimal residual disease (MRD) monitoring shows promise for risk stratification and decision-making in cancer patients. However, factors like background noise from non-tumor DNA, clonal haematopoiesis, and non-shedding tumors may complicate manual interpretation and limit its clinical application. In this proof-of-concept study in advanced non-small cell lung cancer (NSCLC) patients treated with immune checkpoint inhibitors (ICIs), we developed an algorithm that automatically classifies serial cell-free DNA (cfDNA) samples, thereby enabling reliable and reproducible interpretation, and preventing time-consuming manual interpretation in approximately 75% of patients. Importantly, application of the algorithm allowed early risk stratification and decision-making, specifically identifying approximately 35% of patients with short-term clinical benefit and approximately 25% of patients who may potentially benefit from treatment escalation. Simultaneous serum tumor marker (STM) monitoring further improved risk stratification and decision-making in our study, enabling accurate identification of all patients with a clinical benefit of at least one year.

  Study EGAS50000001554

• The dataset of Southeast Borneo individuals (Banjar and Ngaju ethnic groups) was used as comparative data to determine the Asian parental population of the Malagasy. Our study found strong support for an origin of the Asian ancestry of Malagasy among the Banjar.

  Malagasy genetic diversity results from an exceptional proto-globalisation process that took place over a thousand years ago across the Indian Ocean. Previous efforts to locate the Asian origin of Malagasy have highlighted Borneo broadly as a potential source, but so far no firm source populations have been identified. Here, we have generated genome-wide data from two Southeast Borneo populations, the Banjar and the Ngaju, together with published data compiled from populations across the Indian Ocean region. We find strong support for an origin of the Asian ancestry of Malagasy among the Banjar. This group emerged from the long-standing presence of a Malay Empire trading post in Southeast Borneo, which favoured admixture between the Malay and an autochthonous Borneo group, the Ma’anyan. Reconciling genetic, historical and linguistic data, we show that the Banjar, in Malay-led voyages, were the most probable Asian source among the analysed groups in the founding of the Malagasy gene pool.

  Study EGAS00001001841

• Molecular Subtyping Reveals Immune Alterations Associated with Progression of Bronchial Premalignant Lesions

  Exposure to cigarette smoke creates a field of injury throughout the entire respiratory tract inducing genomic alterations that lead to an "at-risk" airway where lung cancers develop. Lung squamous cell carcinoma (SCC) arises in the epithelial layer of the bronchial airways and is often preceded by the development of premalignant lesions (PMLs). Effective tools to identify and treat premalignant lesions at highest risk of progression to invasive carcinoma are not available. Endobronchial biopsies and brushings were obtained from high-risk subjects undergoing lung cancer screening at approximately 1-year intervals by white light and auto-fluorescence bronchoscopy and computed tomography at the Roswell Park Cancer Institute in Buffalo, NY. Subjects were selected that had biopsies collected in repeat locations via serial bronchoscopies. mRNA sequencing was performed on a discovery cohort (DC) of samples comprising endobronchial biopsies and brushes collected between 2010 and 2012 (n=30 subjects, n=197 biopsies, and n=91 brushings). mRNA sequencing was subsequently performed on a validation cohort (VC) of samples comprising endobronchial biopsies and brushes collected between 2010 and 2015 (n=20 subjects, n=111 biopsies, and n=49 brushings). Data analysis identified four distinct molecular subtypes (Proliferative, Inflammatory, Secretory, and Normal) in the bronchial biopsies that correspond to a spectrum of biological and morphological alterations. The Proliferative subtype was enriched with dysplastic PMLs from current smokers that exhibit up-regulation of metabolic and cell cycle pathways and down-regulation of cilium-associated processes. Molecular subtype classification in the validation cohort biopsies replicated these significant clinical and biological associations. Airway brushes from normal fluorescing areas of the large airway classified as the Proliferative subtype specifically predict the presence of biopsies of this same subtype. Within the Proliferative subtype, genes associated with interferon signaling and antigen processing and presentation were observed to be down-regulated among dysplastic biopsies that persist or progress in the future. Innate and adaptive immune cells were computationally predicted to be depleted in these biopsies and this was confirmed via immunofluorescence staining of adjacent biopsies. These findings provide a proof of concept that molecular biomarkers of endobronchial biopsies can enhance histopathological grading and that immunoprevention strategies are an important future direction in intercepting the progression of PMLs to lung cancer.FASTQ files from the RNA sequencing of these biopsies and brushings will be available via dbGaP.

  Study phs003185

• The_GENCODE_exome___sequencing_the_complete_human_exome

  We report the design of an extended set of targets for capturing the complete human exome, based on annotation from the GENCODE consortium. The extended set covers an addition 5,594 genes and 10.3 Mb compared to current sets which mainly target the CCDS database. The additional regions include potential disease genes previously inaccessible to exome resequencing studies, such as 43 genes linked to ion channel activity and 70 genes linked to protein kinase activity. In total, the new GENCODE exome set developed covers 47.9Mb and performed well in sequence capture experiments with HapMap and clinical samples. Samples within this study are prepared with either the CCDS or GENCODE exome products.

  Study EGAS00001000016

• FaceBase Study of Facial Shape in Tanzania: CIDR

  The goals of this project are to identify loci that underlie major genetic determinants of orofacial shape, by means of a GWAS in a cohort of normal African children (from Tanzania) from whom we have collected 3D digitized facial morphometric scans, and a subsequent replication study of normal children from the same population. These studies are part of the NIDCR FaceBase initiative (https://www.facebase.org/). In addition to dbGaP, all study genotype and phenotype data (including primary facial scans and landmarks) will be available for data-sharing with qualified investigators via the NIDCR FaceBase Hub (www.facebase.org/), following approval by the NIDCR FaceBase Data Access Committee.

  Study phs000622

• Breast Cancer Risk Pathways

  We sought to identify genomic variants that differed between individuals who developed familial breast cancer and individuals who had a family history of breast cancer but who had not developed breast cancer. We aggregated these data at the pathway level to identify pathways that play a role in familial breast cancer development. We profiled peripheral blood cells, extracted DNA, and sequenced the DNA using exome-capture sequencing to identify genomic variants in these samples. For 34 of the 35 samples, we also profiled peripheral blood using Affymetrix Human Exon 1.0 ST Array microarrays. Those data can be found in Gene Expression Omnibus under accession identifier GSE47862.

  Study phs001044

• Genome-wide chromatin accessibility profiling of primary human glomerular and kidney cortex tubular outgrowth cultures

  We generated primary cultures from mechanically isolated kidney glomeruli (filtration unit of the nephron) which are composed of podocytes and mesangial cells. In parallel, we generated primary kidney cortex tubule cell cultures, which are composed primarily of proximal tubule cells. Early passage cultures of these two cell types were subjected to chromatin accessibility profiling (DNase-Seq) and gene expression profiling (RNA-Seq). We found thousands of dynamically regulated enhancers in both cell types that potentially regulate nearby and distal target genes that are differentially expressed. These data will be useful for understanding the epigenomic regulation of gene transcription in key kidney cell types.

  Study phs001720

• GWAS in Fibrosing Interstitial Lung Disease

  This study was a case-control genome-wide association study of 1616 non-Hispanic white cases and 4683 controls. Under an additive model for the minor allele at each SNP, we identified 19 SNPs, representing 7 chromosomal locations (5p15, 6p24, 7q22, 11p15, 15q14-15, 17q21, and 19p13), with genome-wide significant (P < 5x10-8) associations using the discovery samples included in this submission. We genotyped the 19 genome-wide significant SNPs in addition to 178 SNPs with 5x10-8 < P-value <.0001 and found 4 additional loci (3q26, 4q22, 10q24, and13q34) with genome-wide significant SNPs in the meta-analysis.

  Study phs000751

• DNA methylation in rhabdomyosarcoma PDX and PDX-derived primary cells

  Conditions to maintain primary tumor cells in culture are largely unknown for most tumor entities including rhabdomyosarcoma. In this collaborative study with Dr. Beat Schäfer's laboratory, we performed DNA methylation profiles of rhabdomyosarcoma patient-derived xenograft (PDX) and their matching PDX-derived primary cells (PPC), where the PPCs were developed and maintained under optimized culture conditions. We further compared DNA methylation profiles between these PDXs and PPCs. Exome sequencing and copy number analysis between these rhabdomyosarcoma PDXs and PPXs were also carried out. These analyses may help us to evaluate a feasibility of in vitro profiling of primary rhabdomyosarcoma cells from a genomic perspective.

  Study phs002051

• Mechanisms of Chemotherapy Resistance in T-ALL

  The goals of this study are to unravel the molecular mechanisms underlying leukemic transformation and chemotherapy resistance in T-cell acute lymphoblastic leukemia (T-ALL). Towards this end, a cohort of T-ALL lymphoblast specimens was collected at the time of initial T-ALL diagnosis (prior to the start of therapy) from children enrolled on contemporary clinical trials, Children's Oncology Group study AALL0434 and Dana-Farber Cancer Institute 05-001. Samples were analyzed using targeted exon sequencing and RNA sequencing analysis. Results of these analyses form the basis of studies that have been submitted for publication, and will be linked to this entry once published.

  Study phs001513

• DNA Methylation age and mortality in the Lothian Birth Cohorts of 1921 and 1936

  The study examined the association between DNA methylation age and mortality. Methylation age was estimated in 4 cohorts (including the Lothian Birth Cohorts of 1921 and 1936) and related to subsequent time-to-death. Across all four cohorts there was a strong correlation between predicted methylation age and chronological age. For individuals with a 5 year age acceleration (DNA methylation age - chronological age = 5), there was a meta analysed hazard ratio of mortality of 1.21 [1.14, 1.29]. Phenotype data associated with the study are available through dbGaP, the methylation raw data are available through the European Genome-phenome Archive (EGA; accession number EGAS00001000910).

  Study phs000821

• NHLBI TOPMed: Childhood Asthma Management Program (CAMP)

  The Childhood Asthma Management Program (CAMP) was designed to evaluate whether continuous, long-term treatment (over a period of four to six years) with either an inhaled corticosteroid (budesonide) or an inhaled noncorticosteroid drug (nedocromil) safely produces an improvement in lung growth as compared with treatment for symptoms only (with albuterol and, if necessary, prednisone, administered as needed). The primary outcome in the study was lung growth, as assessed by the change in forced expiratory volume in one second (FEV1, expressed as a percentage of the predicted value) after the administration of a bronchodilator. Secondary outcomes included the degree of airway responsiveness, morbidity, physical growth, and psychological development.

  Study phs001726

• Single-cell characterization of human GBM reveals regional differences in tumor-infiltrating leukocyte activation

  Background: Glioblastoma (GBM) harbors a highly immunosuppressive tumor microenvironment (TME) which influences glioma growth. Major efforts have been undertaken to describe the TME on a single-cell level. However, human data on regional differences within the TME remain scarce. Goals: we performed single-cell RNA sequencing (scRNAseq) on paired biopsies from the tumor center, peripheral infiltration zone and blood of five patients with primary GBM Details: This EGA study includes raw data sequencing files for the scRNA-seq samples. The processed data (output from Alevin, UMI count matrix and cell metadata) are available from GEO https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE197543

  Study EGAS50000000302

• Characterizing the secretome of licensed hiPSC-derived MSCs

  Although mesenchymal stromal cells (MSCs) from primary tissues have been successfully applied in the clinic, their expansion capabilities are limited and results are variable. MSCs derived from human-induced pluripotent stem cells (hiMSCs) are expected to overcome these limitations and serve as a reproducible and sustainable cell source. We have explored characteristics and therapeutic potential of hiMSCs in comparison to hBMSCs. Our data qualify hiMSCs as a promising source for cell therapy and/or cell-based therapeutic products. Additionally, the herewith generated database will add to our understanding of the mode of action of regenerative cell-based therapies and could be used to identify relevant potency markers.

  Study EGAS50000000389

• Dynamics of tumor ecosystems and microbiome in response to neoadjuvant atezolizumab, bevacizumab, and FOLFOX treatment in patients with unresectable colorectal cancer with liver metastasis

  This study aims to explore the effects of neoadjuvant atezolizumab, bevacizumab, leucovorin, 5-fluorouracil, and oxaliplatin (ABFOLFOX) in patients with unresectable colorectal liver metastases (CRLM), focusing on the molecular dynamics of tumor ecosystems (TE) of CRLM and their impact on treatment outcomes. The study comprises two cohorts with CRLM tissue samples analyzed with RNA sequencing and immunohistochemical staining: cross-sectional cohort A (n = 60, CRLM treated with or without neoadjuvant chemotherapy) and prospective cohort B (n = 20 with serial sampling and treated with ABFOLFOX). Shotgun metagenomic sequencing was done for stool samples from cohort B.

  Study EGAS50000000677

• Clinical evaluation of long read sequencing-based episignature detection in developmental disorders

  Some developmental disorders (DD) are marked by specific genome-wide methylation changes, known as episignatures, which can support diagnosis and reveal underlying mechanisms. Current methods rely on indirect methylation profiling. Here, we assessed whether long-read whole genome sequencing with nanopore technology could directly detect both episignatures and genetic variants. We sequenced forty controls and twenty DD patients, using clustering and dimensional reduction to compare methylome patterns with microarray-based signatures. Our classifiers accurately identified episignatures in 17 of 19 patients with pathogenic variants, matching microarray results. This study shows nanopore sequencing enables comprehensive, haplotype-aware genomic and epigenomic analysis for DD diagnostics.

  Study EGAS50000000719

• Bulk RNAseq - Calprotectin in vitro effects on human early hematopoiesis

  To explore the effects of calprotectin (CAL) on early hematopoiesis, we incubated CD34+ cells from four healthy donors for 7 days in the presence of stem cell factor (SCF), FLT3-ligand and thrombopoietin (TPO) without and with CAL, interleukin-6 (IL6) and the IL6_CAL combination before collecting cells. We performed the same experiment with CD34+ cells collected from three patients with JAK2-V617F-mediated myelofibrosis (MF). A total of 135,545 cells from healthy donors and 111,725 cells from myelofibrosis patients were analyzed by single-cell RNA sequencing (scRNA-seq) using the 10X Chromium droplet-based platform. Bulk RNAseq 4 conditons : -Control - Calprotectin - IL-6 - Calprotectin+IL-6

  Study EGAS50000000454

• Assessing Individual Head and Neck Squamous Cell Carcinoma Patient Response to Therapy Through Integration of Functional and Genomic Data

  This study combines RNA sequencing (RNASeq), whole exome sequencing (WES), reverse phase protein array (RPPA) and copy number variation (CNV) data, along with a custom high throughput inhibitor assay to characterize tumor cells from patients with head and neck squamous cell carcinoma (HNSCC), in order to identify potential therapy targets on an individual patient basis. The data that will be available through dbGaP include the RNASeq, WES, RPPA and array CNV data for the tumor and matched normal samples. This study represents a proof-of-concept. No treatments were administered to patients as part of this study.

  Study phs003456

• Single-Cell Transcriptomic Characterization of Microscopic Colitis

  Patients with microscopic colitis (MC), chronic diarrhea without histological signs of MC, or unaffected controls were profiled using single-cell RNA sequencing (scRNA-seq; inDrops and 10X Genomics were used). One profiled patient without clinical symptoms was found to have histological signs of MC (asymptomatic MC). Some of the subjects from dbGaP study phs003418 are controls in this study. T-Cell Receptor sequencing (TCR-Seq) was also performed on a subset of patients. Individual transcriptomes were analyzed to characterize the cellular profile associated with MC and search for mediators of disease pathology. Raw reads and processed count matrices will be available through dbGaP.

  Study phs003876

• scRNAseq analysis of CD8 T cells infiltrating the bladder and tumor of 4 non-muscle-invasive bladder cancer patients, before and after BCG treatment.

  We performed scRNAseq analysis of CD8 T cells infiltrating the bladder and tumor of 4 non-muscle-invasive bladder cancer patients, before and after BCG treatment. In order to identify tumor-specific T cells, we selected CD8 T cells that were enriched in the tumor of the patient. We also selected CD8 T cells appearing in the bladder after BCG treatment, with the hypothesis that BCG treatment stimulates tumor-specific CD8 T cells. Next, we cloned the TCR of these T cells in a Jurkat cell line and tested these TCR for recognition of tumor-specific antigens.

  Study EGAS50000001384

• Single-cell RNA sequencing of SI-NET

  Small intestinal neuroendocrine tumors (SI-NETs) arise from hormone-producing cells in the gut, yet the molecular changes driving malignant transformation remain poorly understood. Bulk tissue-based analyses make it challenging to distinguish signals derived from normal cells from those of normal hormone-producing cells. In this study, we analyzed SI-NETs at single-cell resolution and directly compared tumor cells with their corresponding normal hormone-producing counterparts using single-cell RNA sequencing. Tissue samples were obtained from two patients undergoing tumor resection surgery. Cells from corresponding normal intestinal mucosa and SI-NET tumors were isolated using specific markers and analyzed for direct comparison.

  Study EGAS50000001584

• Heritable pulmonary arterial hypertension - new genetic findings and environmental triggers

  Whole exome seqeuncing data were analysed for a total of 13 family members of five heritable pulmonary arterial hypertension (HPAH) families to identify a disease causing variant. In a first step, variants only present in affected family members and absent in healthy relatives of the respective family were selected. Subseqeuntly, due to incomplete penetrance of genes in PAH, the analysis was extended to variants present both in affected and healthy individuals. Heterozygous variants were primarily investigated followed by homozygous, compound heterozygous, and bi-allelic variants of interest. This study led to the identification of rare deleterious variants in three out of five families.

  Study EGAS50000001275

• Tracing the molecular route to progression in miRNA biogenesis-defective thyroid lesions

  Alterations in the DICER1 and DGCR8 microprocessor genes confer risk to the development of benign and malignant thyroid lesions. The involvement of 2 miRNA biogenesis genes in benign and malignant thyroid tumors highlights the key role of miRNAs in the thyroid gland. We traced the progression from benignity to malignancy in DICER1- and DGCR8-mutated thyroid lesions by performing a multiomic characterization of these lesions aiming to uncover unique features characterizing either form for potential use as biomarkers. This multiomic characterization included whole exome sequencing (WES) (N=18), miRNA profiling (N=38), spatial transcriptomics (N=2) and/or methylome (N=281).

  Study EGAS50000001577

• Extracellular vesicles from TGF-β-activated cancer-associated fibroblasts remodel the tumor microenvironment through EV surface-associated proteins.

  In this study, we explored the function of extracellular vesicles (EVs) derived from non-activated cancer-associated fibroblasts (CAFs) and TGF-β-activated CAFs. We tested these two types of EVs on other cell types in the tumor environment, including cancer cells, CD8+ T cells, and CAFs. We further explored the protein cargo in EVs altered by TGF-β treatment using quantitative proteomics, and selected several highly upregulated proteins for further analysis. We found that the majority of these proteins were presented on the EV surface, and they regulated the target cells in an EV-cell contact dependent manner.

  Study EGAS50000000922

• Transcriptome analysis of a novel human iPSC-derived 3D cortical tissue model – 2D versus 3D co-culture comparison

  Single-cell RNA-seq analysis of human iPSC-derived microglia/astrocytes/neurons in a novel, human in vitro 3D cortical tissue model, as well as 2D co-cultures for comparison. Samples include distinct conditions (each as biological triplicates): - wild-type cells from 2D or 3D co-cultures after 3 months of culturing (2D_WT, 3D_WT) - knock-in cells from 2D or 3D co-cultures carrying three familial AD mutations in the APP gene (Swedish, Iberian, Arctic; introduced by CRISPR/Cas9-mediated knock-in) after 3 months of culturing (2D_KI, 3D_KI) - 2D and 3D KI cultures treated with Bumetanide (KI_bum) or BACE IV (KI_bace) inhibitor

  Study EGAS50000001392

• Cardiogenics_re_sequencing

  The Cardiogenics re-sequencing study will consist of three parts: Eight pools of 25 individuals will be sequenced using a Nimblegen hybrid-capture solution specific to miRNA sequences, 80 pools of 25 individuals will be sequenced using a custom Agilent SureSelect array covering genes associated with coronary artery disease (CAD) and myocardial infarction (MI), 10 individuals from families with a history of CAD/MI will be exome sequenced using the Sanger exome array. The experiment will use the early onset patients from the German MI cohort and the UK BHF CAD/MI cohort both of which have strong family history. For controls we will consider individuals from the UKBS and KORA cohorts.

  Study EGAS00001000079

• Genomic and ecologic characteristics of the airway microbial-mucosal complex

  Lung diseases due to infection and dysbiosis affect hundreds of millions of people world-wide. Microbial communities at the airway mucosal barrier are conserved and highly ordered, reflecting symbiosis and co-evolution with human host factors. We show here the results of the first systematic culture and whole-genome sequencing of the principal airway bacterial species. We match the gene content of bacterial isolates to human transcripts and metabolites expressed late in airway epithelial differentiation, identifying pathways that can sustain host interactions with the microbiota. Our results provide a systematic basis for decrypting interactions between commensals, pathogens, and mucosal immunity in lung diseases of global significance.

  Study EGAS00001006689

• Use_of_Deep_Sequencing_to_Dectect_Clonal_Mutations_In_Sun_Exposed_Skin_Epidermis

  This study aims to define the landscape of somatic mutations in sun exposed human skin by deep sequencing, analyse their frequency and use the data to infer the effect of mutations on proliferating cell behaviour. The frequency of each mutation will reflect the size of the clone of cells in the tissue sample. By analyzing small samples, clones with as few as 100 cells will be detectable. Allele frequency distributions for each mutation will be used to infer cell fate using published methods (Klein et al. 2010). This study will shed unprecedented light on the early clonal events that lead to the emergence of cancer.

  Study EGAS00001000515

• Molecular Characterization of ETMRs

  ETMRs are poorly characterized embryonal brain tumors with a dismal outcome. We collected tumors from 184 ETMR patients and 23 matched recurrences to investigate the genomic landscape of this distinct entity. Tumors without C19MC amplification, the proposed driver, harbor other miRNA related aberrations like DICER1 mutations and amplifications of the MIR17-92 miRNA cluster. All tumors behave molecularly similar and no subgrouping was observed. Whole-genome sequencing revealed an overall low recurrence of SNVs, but highly prevalent R-loop associated genomic instability. Finally, we show that targeting R-loops with TOP1 and PARP inhibitors might be an effective treatment strategy for this deadly disease.

  Study EGAS00001003256

• Inter and intra - tumor heterogeneity in Colorectal Cancer

  We used high depth massive parallel sequencing analyses to study 27 CRC (colorectal cancer) patients, with a total of 97 tumors (both primary and matched metastases) in addition to healthy control samples. We found inter-tumor concordance for coding mutations; in contrast, gene copy numbers were found to be highly discordant between primary tumors and metastases as validated by fluorescent in-situ hybridization. in a further step, we dissected a single tumor into 68 spatially defined samples and sequenced them separately. Here we identify evenly distributed coding mutations in APC and TP53 in all tumor areas, yet highly variable gene copy numbers in numerous genes.

  Study EGAS00001002150

• Exome-wide analysis identifies three low-frequency missense variants associated with pancreatic cancer risk in Chinese populations

  Germline coding variants have not been systematically investigated for pancreatic ductal adenocarcinoma (PDAC). Here, we report an exome-wide investigation using the Illumina Human Exome Beadchip with 943 PDAC cases and 3,908 controls in the Chinese population, followed by two independent replicate samples including 2,142 cases and 4,697 controls. We identify three low-frequency missense variants associated with the PDAC risk: rs34309238 in PKN1 (OR = 1.77, 95% CI: 1.48-2.12, P = 5.35 X 10-10), rs2242241 in DOK2 (OR = 1.85, 95% CI: 1.50-2.27, P = 4.34 X 10-9) and rs183117027 in APOB (OR = 2.34, 95% CI: 1.72-3.16, P = 4.21 X 10-8).

  Study EGAS00001003040

• Use_of_Deep_Sequencing_to_Dectect_Clonal_Mutations_In_Sun_Exposed_Skin_Epidermis_PART2

  This study aims to define the landscape of somatic mutations in sun exposed human skin by deep sequencing, analyse their frequency and use the data to infer the effect of mutations on proliferating cell behaviour. The frequency of each mutation will reflect the size of the clone of cells in the tissue sample. By analyzing small samples, clones with as few as 100 cells will be detectable. Allele frequency distributions for each mutation will be used to infer cell fate using published methods (Klein et al. 2010). This study will shed unprecedented light on the early clonal events that lead to the emergence of cancer.

  Study EGAS00001000603

• Investigating_low_frequency_variants_in_CAD_MI_cases__controls_and_pedigrees_using_whole_exome_sequencing_and_custom_pulldowns

  The Cardiogenics re-sequencing study will consist of three parts: Eight pools of 25 individuals will be sequenced using a Nimblegen hybrid-capture solution specific to miRNA sequences, 80 pools of 25 individuals will be sequenced using a custom Agilent SureSelect array covering genes associated with coronary artery disease (CAD) and myocardial infarction (MI), 10 individuals from families with a history of CAD/MI will be exome sequenced using the Sanger exome array. The experiment will use the early onset patients from the German MI cohort and the UK BHF CAD/MI cohort both of which have strong family history. For controls we will consider individuals from the UKBS and KORA cohorts.

  Study EGAS00001000043

• Investigating_low_frequency_variants_in_CAD_MI_cases__controls_and_pedigrees_using_whole_exome_sequencing_and_custom_pulldowns

  The Cardiogenics re-sequencing study will consist of three parts: Eight pools of 25 individuals will be sequenced using a Nimblegen hybrid-capture solution specific to miRNA sequences, 80 pools of 25 individuals will be sequenced using a custom Agilent SureSelect array covering genes associated with coronary artery disease (CAD) and myocardial infarction (MI), 10 individuals from families with a history of CAD/MI will be exome sequenced using the Sanger exome array. The experiment will use the early onset patients from the German MI cohort and the UK BHF CAD/MI cohort both of which have strong family history. For controls we will consider individuals from the UKBS and KORA cohorts.

  Study EGAS00001000050

• MutWP5__CRUK_Mutographs_of_Cancer__Lung__PD38234__Targeted_

  Sequencing of LCM-derived microbiopsies from explanted lung from pulmonary fibrosis patient. Goal to assess the mutational burden, spectrum, and clonal dynamics within the tissue. Deep sampling throughout multiple regions of the lung will determine whether there are differences in smoking-related mutation burden in different portions of the lung. Targeted sequencing will be conducted on samples to identify drivers of interest and clonality of the samples, well-performing samples will be sent for subsequent whole-genome sequencing. Results from this portion of the study will be compared to other individuals with smoking-related diseases (COPD, pulmonary fibrosis, lung cancer), and normal, non-smoking lungs.

  Study EGAS00001003325

• SNV and indel calls from 8921 individuals in the British Autozygosity Populations BioResource dataset

  This includes variant calls (single nucleotide variants and small insertions/deletions) from 8086 (mostly British Pakistani/British Bangladeshi) individuals from the following studies: 1. 5236 British Pakistani/British Bangladeshi adults from East London Genes and Health (ELGH) 2. 2624 British South Asian mothers from Born in Bradford (mostly Pakistani) (BiB) 3. 1061 British South Asian adults from Birmingham (mostly Pakistani) (Birm) All of the Birmingham and most of the Born in Bradford samples were previously sequenced as part of PMID: 26940866. In the sample list file, the columns of interest to most people will be: vcf.id - sample ID from the vcf cohort - which cohort they're in sex.assigned - sex inferred from coverage on the X and Y chromosomes. Individuals for whom this did not match their reported sex have been discarded total, chrX and chrY - coverage within bait regions across all chromosomes, chrX and chrY respectively Mapping was done with bwa-mem and variant calling was carried out with GATK HaplotypeCaller. We removed variant sites for which the following was true: SNPs: "QD < 2.0 || FS > 30 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0" Indels: "QD < 2.0 || FS > 30 || ReadPosRankSum < -20.0"

  Dataset EGAD00001005469

• RNA sequencing in primary human macrophages overexpressing ETS2

  This dataset consists of RNA sequencing data from an ETS2 overexpression experiment in M0 macrophages. Controlled overexpression of ETS2 mRNA or control mRNA (an equivalent amount of mRNA encoding the reverse complement of ETS2 – thereby controlling for the quantity, length and purine/pyrimidine composition of the transfected RNA but with a transcript that would not be translated) was induced in resting, non-activated (M0) macrophages by transfecting predefined amounts of in vitro transcribed mRNA. To minimise non-specific activation due to the transfected RNA, in vitro transcription was performed using co-transcriptional capping (to minimise uncapped products), and incorporating modified, minimally immunogenic nucleotides (replacing uridine with N1-methyl-pseudouridine and cytidine with methylcytidine). After 18 hours, transfected cells were were activated with low dose LPS and harvested for RNA-sequencing 6 hours later. Sequencing libraries were prepared from 10ng RNA using the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara) following the manufacturer’s instructions. The quality and molarity of all libraries was assessed using a BioAnalyzer 2100 and the libraries were sequenced on a NovaSeq6000. Raw data are provided as 100 bp paired-end Illumina reads from n = 8 donors.

  Dataset EGAD00001011341

• The dataset for Detection and characterization of lung cancer using cell-free DNA fragmentomes

  The dataset for Detection and characterization of lung cancer using cell-free DNA fragmentomes includes 872 bam files from whole genome next-generation sequencing on the Illumina HiSeq2500. The samples analyzed include plasma samples from healthy individuals and patients with cancer.

  Dataset EGAD00001007796

• Diet driven microbial ecology underpins associations between cancer immunotherapy outcomes and the gut microbiome

  This study profiled baseline gut (fecal) microbiota signatures and dietary patterns of 103 trial patients from Australia and the Netherlands treated with neoadjuvant ICIs for high risk resectable metastatic melanoma and performed an integrated analysis with data from 115 patients with melanoma treated with ICIs in the United States. We observed geographically distinct microbial signatures of response and immune-related adverse events. Overall, response rates were higher in Ruminococcaceae-dominated microbiomes than in Bacteroidaceae-dominated microbiomes. Poor response was associated with lower fiber and omega 3 fatty acid consumption and elevated levels of C-reactive protein in the peripheral circulation at baseline.

  Study EGAS00001006982

• Comprehensive Deep Sequencing Atlas in HCC tumors

  Establishment of a comprehensive deep sequencing atlas focused on Hepatocellular Carcinoma (HCC) tumors, employing Whole Genome Sequencing (WGS), RNA Sequencing (RNAseq), and Whole Exome Sequencing (WES). The atlas aims to unravel the intricate genetic landscape of HCC, providing a detailed characterization of genomic alterations, transcriptomic profiles, and key mutations associated with this liver cancer. The integration of WGS, RNAseq, and WES data offers a holistic perspective, facilitating a deeper understanding of the molecular mechanisms driving HCC pathogenesis. The resulting atlas serves as a valuable resource for researchers, clinicians, and the broader scientific community, contributing to advancements in HCC diagnostics, prognostics, and therapeutic interventions.

  Study EGAS00001007694

• Single cell epigenomic study of H3-K27M mutant diffuse midline glioma across age and location

  Histone 3 lysine27-to-methionine (H3-K27M) mutations most frequently occur in childhood diffuse midline gliomas (DMGs) of the pons, but are also increasingly recognized in adult DMGs. Their potential heterogeneity at different ages and midline locations are vastly understudied. Here, through dissecting the single-cell epigenomic architectures of a comprehensive cohort of patient H3-K27M DMGs, we delineate how age and anatomical location shape glioma cell-intrinsic and -extrinsic features in light of the shared driver mutation. We analyzed the open chromatin profiles of 8 tumors utilizing the single-cell/nucleus assay for transposase-accessible chromatin using sequencing (snATAC-seq)

  Study EGAS00001007035

• Single-cell profiling of neoantigen-specific T cells in lung cancers treated with neoadjuvant PD-1 blockade

  We study the expression profile of MANA-specific T cells, we used the MANA functional expansion of specific T cells (MANAFEST) assay in neoadjuvant anti-PD-1-treated lung cancers and applied their T cell receptor’s (TCR) complementarity-determining region 3 (CDR3) as a “barcode” to track and analyze their transcriptional programs in the tumor microenvironment using single cell TCR sequencing coupled with single cell RNA sequencing. We revealed distinct phenotype for MANA- and virus-specific clones in TIL and adjacent normal lung, regardless of response. MANA-specific T cells show features that drive the differences between responders and non-responders.

  Study EGAS00001005343

• Papua New Guinean Lowlanders dataset

  The Papua New Guinean Lowlanders dataset includes 41 whole genome sequences for Papua New Guinean individuals sampled in Daru. DNA was extracted from saliva samples (Oragen kit). Sequencing libraries were prepared using the TruSeq DNA PCR-Free HT kit. 150 bp paired-end sequencing was performed on the Illumina HiSeq X5 sequencer. The PGAP dataset provides Fastq, mapped cram files (GRCh38) and phenotype measurements.

  Dataset EGAD50000000050

• 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

• mRNA-Sequencing of 73 primary multiple myeloma (MM) samples and human MM cell lines

  mRNA-Sequencing of 73 primary multiple myeloma (MM) samples and human MM cell lines before and after siRNA-mediated knockdown of ADAM8 (n=5 cell lines), ADAM9 (n=7 cell lines) and ADAM15 (n=5 cell lines). Paired-end sequencing was performed on a NovaSeq (Illumina). Fastq and bam files are provided for each sample.

  Dataset EGAD50000000575

• Genetic subtyping by Whole Exome Sequencing across Diffuse Large B Cell Lymphoma and Plasmablastic Lymphoma.

  Whole exome sequencing was performed from 108 Diffuse Large B Cell Lymphoma cases. A library containing whole exome regions was used to isolate the DNA for sequencing (SureSelect XT Human All Exon V6 (Agilent technologies)). Sequencing on a NovaSeq 6000 instrument (Illumina, paired end, 2x100, mean 566Gb per FlowCell) was performed.

  Dataset EGAD50000000546

• 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

• Dataset for WGS and RNA samples of acute myeloid leukemia with MNX1 expression

  This dataset contains 10 samples of WGS, ATAC, 4C and RNAseq samples of patients with acute myeloid leukemia. The sequencing was performed on Illumina HiSeq 4000, 2000 and HiSeq X using Illumina TruSeq Nano DNA and Agilent Strand Specific RNA Kits. The sequencing was always paired.

  Dataset EGAD50000001098

• Clinical and demographics data from IMvigor210, IMvigor211, IMvigor130 and IMvigor010

  Clinical data include demographics (gender, race), specimen type (primary vs. metastatic), tract (upper vs. lower), liver metastasis status, PD-L1 IHC, tumor mutation burden, CD8 T cell infiltration status, neutrophil enrichment score, treatment arm, objective response rate, overall survival and progression free survival, and ctDNA status (IMvigor010 only) for 2803 patients across the four IMvigor trials.

  Dataset EGAD50000001101

• Bulk RNA-sequencing data from five lines of human iPSC-derived (hiPSC-derived) astrocytes, both alone and in co-culture with neurons, to define the molecular response of astrocytes to misfolded alpha-synuclein.

  Samples were derived from five lines of human iPSC-derived (hiPSC-derived) astrocytes, both alone and in co-culture with neurons +/- alpha-synuclein oligomer treatment. Paired-end FASTQ files for each of the samples are provided.

  Dataset EGAD50000001109

• WES IDC samples

  PDX samples of breast cancer IDC mouse models created from patient tumor material of the NKI. Genomescan prepared the samples according to the procedure for Hybridization Capture using the Agilent SureSelectXT Human All Exon V7 kit. The prepared libraries were sequenced with Illumina sequencing technology. The samples are in fastq format and consist of the following PDX samples: IDC001, IDC125, IDC147, IDC200, IDC233, IDC244, IDC251, IDC272, IDC278, IDC281 and ILC120.

  Dataset EGAD50000001148

• MOSAIC Window Glioblastoma Data

  This dataset will include Spatial Transcriptomics, Single-Cell RNA-Seq, Bulk RNA-Seq, Clinical data, WES, and H&E data from 10 Glioblastoma (GBM) Cancer patients. Researchers from private or public institutions outside the MOSAIC Consortium will be able to apply to access this data and, pending approval, use the data for their research.

  Dataset EGAD50000001352

• Total RNAseq data from 8 patients with muscle invasive bladder cancer

  For this dataset we performed total RNAseq on blood samples from 8 patients with muscle invasive bladder cancer. The data consists of 8 sets of paired fastq files with accompanying UMI fastq files. Sequenced on the Illumina NoveSeq6000 platform using S2 flow cells (v1.5,2x150 cycles), with a mean yield of 313 million reads.

  Dataset EGAD50000001380

• NSCLC ctDNA multigenic panel

  We analyzed cfDNA plasma samples of subjects with non-small cell lung cancer: treatment naïve (n=24) and prior-treated (n=8). Driver variants for 11 genes was available with Oncomine Lung cfDNA Assay, were assessed by Next-Generation Sequecing. Sequencing data were pre-processed in Ion S5 Torrent Server and aligned to the hg19 human reference genome. Variant calls were performed by IonReporter 5.10 software.

  Dataset EGAD50000000908