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• BLUEPRINT September 2016, ChIPmentation Acute Lymphocytic Leukemia from bone marrow, on Genome GRCh38

  ChIPmentation data for 1 sample(s) Acute Lymphocytic Leukemia from bone marrow, on Genome GRCh38. 2 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT (September 2016).

  Dataset EGAD00001002930

• BLUEPRINT September 2016, ChIPmentation Lymphoma_Follicular from lymph node, on Genome GRCh38

  ChIPmentation data for 3 sample(s) Lymphoma_Follicular from lymph node, on Genome GRCh38. 7 run(s), 6 experiment(s), 6 alignment(s). Part of BLUEPRINT (September 2016).

  Dataset EGAD00001002931

• BLUEPRINT September 2016, ChIPmentation Burkitt Lymphoma from lymph node, on Genome GRCh38

  ChIPmentation data for 3 sample(s) Burkitt Lymphoma from lymph node, on Genome GRCh38. 10 run(s), 8 experiment(s), 8 alignment(s). Part of BLUEPRINT (September 2016).

  Dataset EGAD00001002939

• BCG Molecular Subtyping

  Dataset for the paper: Non-muscle Invasive Bladder Cancer Molecular Subtypes Predict Differential Response to Intravesical Bacillus Calmette-Guérin

  Dataset EGAD00001010065

• Sequencing data for oesophageal and related samples - Nowicki-Osuch, Zhuang et al (scRNA)

  Data supporting: “Single-cell RNA sequencing unifies developmental programs of Esophageal and Gastric Intestinal Metaplasia.” Nowicki-Osuch, Zhuang et al. scRNAseq (FASTQ files) 59 samples

  Dataset EGAD00001010074

• Whole exome and targeted sequencing data from glioblastoma multiforme samples

  Whole exome and targeted sequencing data from 11 glioblastoma multiforme patients. A total of 70 tumour specimens and 11 blood samples were used for whole exome sequencing (WES) using the Agilent SureSelectXT Human All Exon V5 Kit. Two custom targeted sequencing panels were designed using the using Agilent’s Haloplex (TES1) or Agilent SureSelect XT2 technology (TES2). Libraries were sequenced on an Illumina HiSeq2500

  Dataset EGAD00001004420

• Human Embryonic Multi-tissue ChIP-seq (Manchester)

  Histone ChIP-seq of 13 human embryonic tissues from weeks 6-8 of gestation. H3K4me3, H3K27me3 and H3K27ac. Biological replicates (n=2) for 11 tissues. Tissues (n): Brain (2); Retinal Pigmented Epithelium (eye)(2); Palate(2); Tongue (1); Left ventricle (heart)(2); Lung(2); Liver(2); Pancreas (2*); Stomach(1); Upper limb (2); Lower limb (2); Adrenal gland (2); Kidney (2)

  Dataset EGAD00001004335

• OxyTarget mtDNA seq

  We studied 44 rectal cancer patients enrolled onto a prospective population-based biomarker study, who were planned for curative-intent radiation therapy before definitive surgery, yet at high risk of metastatic progression beyond the pelvic cavity. The patients had full-length mtDNA sequencing of whole blood (WB) and peripheral blood mononuclear cells (PBMC), sampled at the time of diagnosis. Metastatic events were recorded up to 60 months of follow-up after completion of the multimodal treatment.

  Dataset EGAD00001007992

• Genomic abnormalities of TP53 define distinct risk groups of paediatric B-cell non-Hodgkin lymphoma

  Whole exome sequencing data from 90 diagnostic lymphoma samples run and published as part of the Leukemia manuscript. 133 total exomes were sequenced including tumour and normal controls. Copy number array data was also generated for 95 patients.

  Dataset EGAD00001008162

• RNAseq and ATACseq data

  RNAseq and ATACseq data for the FMF patients and healthy control. The RNAseq data was sequenced on a BGI MGI G400 machine, with PE100 reads. ATAC-seq libraries were prepared with Illumina Nextera primers and sequenced on NovaSeq 6000 platform with 50bp paired-end sequencing, where each sample was sequenced to approximate 60 million reads.

  Dataset EGAD00001010304

• Validation of Exome-sequencing of S7RE-iPSC lines

  PCR products were obtained from each target loci using genomic DNA from human iPS cells. Subsequently, PCR products are pooled and subjected to Illumina library preparation. The library will be sequenced either by HiSeq or MiSeq. 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 EGAD00001001449

• RNA-seq of multiple myeloma patient samples

  RNA from CD138+ plasma cells from patients with a plasma cell dyscrasia were sequenced using the TruSeq Stranded Total RNA Ribo-zero Gold kit (Illumina). Paired-end 75bp reads were generated on a NextSeq500 or HiSeq4000 (Illumina). The dataset consists of 1 MGUS sample, 5 SMM samples, 69 newly diagnosed myeloma samples, 1 relapsed myeloma sample, 1 previously treated myeloma samples, and 4 PCL samples. Matching whole genome sequencing data are available for these samples under study EGAS00001003164.

  Dataset EGAD00001004543

• Raw sequencing data for donor and patient fecal samples

  Microbiome analysis was performed on the patient samples collected pre-FMT and on days after FMT, and on samples collected from the FMT donor. Genomic bacterial DNA was extracted from fecal samples using the QIAamp DNA Stool kit (Qiagen, Hilden, Germany), with the addition of a bead-beating lysis step. Genomic 16S ribosomal-RNA V4 variable regions were amplified and sequenced on the Illumina MiSeq platform.

  Dataset EGAD00001004371

• RNA sequencing of multiple tumor biopsies and patient-derived spheroids from five colorectal cancer patients (BAM files)

  Whole transcriptome, strand-specific RNA-seq libraries were prepared from total RNA purified using RNeasy mini kit (Qiagen) using Ribo-Zero technology (Epicentre, an Illumina company) for depletion of rRNA followed by library preparation using ScriptSeq ScriptSeq RNA-Seq Library preparation Kit from Illumina. The paired raw sequence reads were processed using TopHat2 and mapped to the humane reference genome HG19.

  Dataset EGAD00001003820

• Low-coverage Whole Genome Sequencing, Colorectal adenomas, NKI-AvL TGO series Stool-Proteomics

  For this tissue dataset, we applied low-pass whole genome sequencing to 98 non-advanced and advanced adenomas. As small number of lesions was sequenced multiple times, this dataset consists of 103 fastq files. These adenomas were classified as lesions with low-risk or high-risk of progression, according to the presence of specific DNA copy number changes (Carvalho et al, CancerPrevRes, 2018).

  Dataset EGAD00001004075

• Susceptibility genes for the development of SLE during treatment of IBD

  A potential and very serious side effect of treating IBD with antiTNFa therapies (the currentgold standard) is the development of systemic lupus erythematosis (SLE). This side effect israre and unpredictable. Out of several thousand cases having received treatment, theUniversity of Calgary have accumulated 12 individuals with full phenotyping and novelserological antibody discovery panel data. We propose to exome sequence these samples inan effort to identify rare highly-penetrant variants that could be underlying this severephenotype.

  Dataset EGAD00001000670

• CCA Visium spatial transcriptomics data (4 CCA)

  Visium spatial transcriptomics (10X Genomics) performed on 4 CCA samples. Each sample has two paired-end sequencing runs: the first (I1 & I2) are a pair reading indexes; the second (R1 & R2) are a pair reading inserts, with R1 additionally reading 10X barcodes. For histology images, please contact authors.

  Dataset EGAD00001011997

• Sequencing data for ICGC Oesophageal Adenocarcinoma tissue samples - mobile_elements

  Samples from Edwards et al 2015 - doi:10.1186/s12864-015-1685-z

  Dataset EGAD00001001048

• Single cell RNA sequencing of colorectal cancer

  To understand intrinsic cancer cell signatures and the surrounding microenvironemt and their interactions, we performed single-cell RNA sequencing on 63,689 cells from 23 patients with 23 primary colorectal cancer and 10 matched normal mucosa samples. Analyzing of primary colorectal cancer and normal mucosa samples show a comprehensive cellular landscape of colon cancer, which is a valuable resource for the development of therapeutic strategies.

  Dataset EGAD00001005198

• Whole exome sequencing of advanced gastric cancer

  To define the cellular characteristics of malignant ascites of advanced gastric cancer patients and search for therapeutic strategies, we obtained 5 malignant ascites and 1 cerebrospinal fluid from five patients with gastric cancer. We analyzed single-cell RNA-seq data of 180 cells from 4 malignant ascites and 1 cerebrospinal fluid metastasis using Fluidigm® C1™ System. Whole exome sequencing data was also generated from blood or tumor tissue.

  Dataset EGAD00001005740

• Somatic whole exome sequencing of a hypermutated gliosarcoma case

  The dataset includes the whole-exome sequencing (WES) of an extramedullary tumor anterior to the spinal cord at T4, which was resected and diagnosed as gliosarcoma. The patient initially diagnosed with a low-grade brain glioma via biopsy, followed by adjuvant radiation and temozolomide treatment. WES was performed using Illumina NovaSeq6000 with 2x100 bp reads. Mean coverage of 152.4x and 230.6x was achieved for normal and tumor, respectively.

  Dataset EGAD00001006816

• Identification of the dismal subtype of B-ALL with dysregulation of CDX2 and UBTF

  PURPOSE: Advance in the knowledge of genomic basis of B-cell acute lymphoblastic leukemia (B-ALL) has changed the treatment approaches and diagnostic assays and improved their outcome. Despite the recent development of next generation sequencing approaches, there are still some cases that their drivers are unknown. We aimed to define and describe the characteristics of an additional B-ALL subtype by integrating genomic, transcriptomic, and epigenomic approach. METHODS: More than 2,000 B-ALL cases of RNA-seq data from from Eastern Cooperative Oncology Group (ECOG) and the American College of Radiology Imaging Network (ACRIN) (n=764), the Children's Oncology Group (COG), Munich Leukemia Laboratory (MLL) (n=280), and other several collaborators were analyzed to identify the new subtype. Whole genome sequence was performed to detect mutations, stractural variants, and copy number alterations. The tridimentional analysis of chromatin was performed with HiChIP. RESULTS: We identified the new high-risk B-ALL subtype “CDX2/UBTF” that exhibited unique gene expression profiles, which is enriched in female (77.3%), adolescents and young adults (52.6%), and relapse cohort (3.3%). CD10 negativity and IgM positivity are hallmarks of this subtype with NTRK3 expression that can be an effective marker at diagnostic approach and a potential targeted therapy with TRK and mulkinase inbitors, larotrectinib and entrectinib. Genetically, two different alterations define CDX2/UBTF. One is UBTF-ATXN7L3 fusions caused by deletion of 17q21.31, and the other is extopic CDX2 expression through the enhancer hijacking mechanism induced by deletion of 13q12.2. Other genomic features include gain of 1q and PAX5 rearrangement (PAX5-ZCCHC7), might induce upregulation of histone cluster genes and PAX5. CONCLUSION: We described the novel B-ALL subtype “CDX2/UBTF” that has unique clinical and genomic characteristics.

  Study EGAS00001005863

• KiCS WGS data for academic and for-profit use

  Data from samples that are marked for both academic and for-profit use.

  Dataset EGAD00001009699

• Genomics of Pediatric Renal Medullary Carcinomas

  Version 1We derived faithful cancer cell lines from patients with a diagnosis of renal medullary carcinomas (RMC). These models have been sequenced with whole genome, exome and transcriptome technologies along with the patient's primary germline and tumor samples. We took these faithful models and performed loss-of-function genetic perturbation screens (e.g. RNAi and CRISPR-Cas9) along with an orthogonal small molecule screen. We identified the ubiquitin-proteasome system as an important target in RMC as well as other SMARCB1 deficient cancers.Version 2We have collaborated with the Children's Oncology Group and the study AREN03B2 to study the cohort of patients with a central diagnosis of RMC. Here, we used 10x linked read sequencing along with RNA-sequencing to profile these matched tumor-normal pairs.

  Study phs001800

• Rapid Acceleration of Diagnostics - Digital Health Technologies (RADx-DHT): COVID-19 Experience Study (C19EX) Survey

  This was conducted virtually through the Achievement studies platform during the current COVID-19 pandemic. Participants were asked to complete a survey every day to capture information about whether they had experienced symptoms corresponding to respiratory, ILI, and COVID-19 infections within the previous 24 hour period, their experiences with the healthcare system, treatments, diagnostic testing, and their behaviors and potential risk factors. Participants were also asked to share their wearable activity tracker data. The purpose of this study was to better understand the geographic spread of diseases, impacts on daily life, and behavioral and physiological functioning in relation to recent self-reported respiratory disease, influenza-like-illness (ILI), and coronavirus disease (COVID-19) events.DOI: https://rapids.ll.mit.edu/10.57895/6m5z-je42

  Study phs002537

• Exome sequencing of autosomal recessive progressive external ophthalmoplegia (arPEO)

  Progressive external ophthalmoplegia (PEO) is an inherited mitochondrial disease that follows either autosomal dominant or recessive forms of inheritance (adPEO or arPEO). AdPEO is a genetically heterogeneous disease and several genes including POLG1 and C10orf2/Twinkle have been identified as responsible genes. On the other hand, POLG1 was the only established gene causing arPEO with mitochondrial DNA deletions. We previously reported a case of PEO with unidentified genetic etiology. The patient was born of a first-cousin marriage. Therefore, the recessive form of inheritance was suspected. To identify the disease causing variant in this patient, we subjected the patient's DNA to whole-exome sequencing and narrowed down the candidate variants using public data and runs of homozygosity analysis.

  Study phs000392

• Gliomas, glioneuronal and neuronal tumors

  The dataset represents a total of 85 DNA samples from 22 male and 20 female pediatric patients affected with gliomas, glioneuronal, and neuronal tumors. The samples were subject to whole genome sequencing, WGS, [71 samples, (representing 18 male and 17 female individuals)] and whole exome sequencing, WES, [14 samples, (representing 4 males and 3 female individuals)]. One tumor tissue sample and one peripheral blood sample were analyzed from each of 84 patients, whereas two tumor tissue samples and one peripheral blood sample were analyzed from one patient. The WGS samples were sequenced 2x150 bp paired-end on an Illumina HiSeqX v2.5 instrument, and the WES samples were sequenced 2x100 bp paired-end on an Illumina HiSeq 2500 instrument. The FASTQ files generated were aligned to the human reference genome sequence GRCh38/hg38 using bwa-mem, with the ALT-aware option turned on. Sorting of reads and marking of PCR duplicates was performed with GATK. Base quality score recalibration and joint realignment of reads around insertions and deletions (indels) were conducted using GATK tools. The dataset consists of 85 files in the CRAM format (lossless compression) with a total file size of ~13,3 TB. Additional genomic and molecular data (FASTQ, BAM, IDAT, and VCF files) and limited clinical data can be requested by ethically approved projects conducting research in the field of pediatric cancer.

  Dataset EGAD50000000300

• Single-cell proteo-genomic reference maps of the human hematopoietic system

  We have generated high content single-cell proteo-genomic reference maps of human blood and bone marrow that quantitatively link the expression of up to 197 surface markers to cellular identities and biological processes across all major hematopoietic cell types in healthy aging and leukemia. Please note raw and integrated gene expression data, cell type annotation, metadata and dimensionality reduction are available as Seurat v3 objects through figshare. Access links are https://figshare.com/s/0fda29b169c719223ee3 (97 surface marker, 9 individuals dataset), https://figshare.com/s/313b5739ff469dac8c01 (197 surface marker, bone marrow and blood dataset), https://figshare.com/s/901bcddb9ee18e226031 (97 surface markers and whole transcriptome dataset) and https://figshare.com/s/24e10bf129fae1918316 (97 surface marker, 15 AML datasets).

  Study EGAS00001005593

• Clonal tracing with somatic epimutations reveals dynamics of blood aging

  In this study, we generated comprehensive single-cell multi-omic datasets from bone marrow samples collected from 13 donors spanning a wide age range. We applied the scTAMseq protocol to profile DNA methylation and nuclear mutations obtained from 7 total bone marrow aspirates (donors A.1-A.7) and 6 CD34+-enriched bone marrow samples ((donors B.1-B.5 & X.1). Complementary surface marker expression data were acquired by integrating CITE-seq into the scTAMseq workflow (scTAMseq_prot). Targeted RNA sequencing (scTAMARA_rna) was performed alongside scTAMARA_DNA on one CD34+-enriched sample (X.1). Additionally, a dedicated mitochondrial panel (TAMITO_seq) was employed on a peripheral blood sample from a healthy donor (X.2) to assess mitochondrial heterogeneity and facilitate lineage tracing.

  Study EGAS00001008056

• Children's Hospital of Philadelphia: GWAS of Left-Sided Cardiac Defects

  This is a family-based genome-wide association study of congenital left-sided cardiac lesions (LSLs). Cases with LSLs and their parents were recruited from the Cardiac Center at The Children's Hospital of Philadelphia between 1997 and 2010. The discovery dataset included 405 LSL case-parent triads. DNA was extracted from blood or saliva samples from these subjects and genotyping was conducted using the Illumina Infinium II HumanHap550K array (V3). This study was conducted with approval from the Institutional Review Board for the Protection of Human Subjects of The Children's Hospital of Philadelphia and all research subjects provided either written informed consent or, when appropriate, assent.

  Study phs000781

• A Genomics-Driven Artificial Intelligence-Based Model Classifies Breast Invasive Lobular Carcinoma and Discovers CDH1 Inactivating Mechanisms

  We developed an artificial intelligence (AI)-model applied to histological images using CDH1 biallelic mutations, pathognomonic for breast invasive lobular carcinoma (ILC), as ground truth. We evaluated the performance of the AI-model to predict the presence of CDH1 biallelic mutations and to diagnose ILC. Subsequently, we investigated the molecular underpinning cases of predicted by the model to harbor a CDH1 biallelic mutations but lacking these alterations according to targeted sequencing. Among this analyses, we subjected to whole genome sequencing (WGS) one ILC case lacking CDH1 biallelic mutations by targeted sequencing and lacking CDH1 promoter methylation to determine the molecular basis of its lobular phenotype.

  Study EGAS50000000485

• DNA Replication Speed controls Epigenome Integrity and T Cell Fate

  Epigenetic mechanisms maintain cellular identities by enforcing stable, cell type-specific transcriptional programs while also allowing regulated plasticity for adaptations to environmental cues like differentiation signals. Dysregulation of this dual capacity has been linked to cancer and chronic inflammation, with the regulatory mechanisms remaining poorly understood. Here, we identify DNA replication speed as a physiological regulator controlling epigenome stability and plasticity. Using T-lymphocytes as a model, we demonstrate that fast DNA replication speed impaired epigenome stability, causing DNA methylation maintenance errors at cell type-specific enhancers and heterochromatin, ultimately leading to compromised cell function. However, accelerated DNA replication speed supported epigenome plasticity during differentiation, promoting successful cell-type transitions

  Study EGAS50000001273

• Single-nuclei histone modification profiling of the adult human central nervous system unveils epigenetic memory of developmental programs

  Here, we profile the adult human CNS from distinct regions, sex and ages, for chromatin accessibility at the single-nuclei level. Tissue was collected from 20 different donors (10 male, 10 female) within the ages of 34 to 74 years old. Each donor donated fresh frozen white matter from the following three tissue regions: primary motor cortex (Brodmann area 4, BA4), arbor vitae cerebelli (CB) and fasciculi cuneatus and gracilis from and cervical spinal cord (CSC). Tissue was processed semi-randomly, ensuring that each batch of experiments had a representation of both sexes and all three tissue regions. Completed libraries were again randomly multiplexed during sequencing to minimize batch effects.

  Study EGAS50000000283

• Whole Mitochondrial DNA sequencing of Gingivo-buccal Cancer : ICGC-India Project

  This dataset pertains to mitochondrial DNA amplicon sequencing of paired DNA samples from gingivo-buccal oral cancer patients. DNA was isolated from the tumor and blood tissues of 89 patients (178 samples). The sequencing libraries were prepared from whole mitochondrial amplicons using Nextera XT DNA Library Preparation Kit (Illumina) and sequenced in Illumina HiSeq platform. The uploaded BAM files are generated by aligning paired-end reads to the mitochondrial reference sequence (rCRS) using BWA-MEM.

  Dataset EGAD00001004987

• Nurminen et al ("GP2Men") Study Primary and Metastatic Prostate Cancer Whole Genome Sequence Data

  We used novel processing techniques to obtain whole genome data together with 3D anatomic and histomorphologic analysis in two men (GP5 and GP12) with high risk PrCa undergoing radical prostatectomy. A total of 22 whole genome-sequenced sites (16 primary cancer foci and 6 lymph node metastatic) were analyzed using evolutionary reconstruction tools and spatio-evolutionary models. Probability models were used to trace spatial and chronological origins of the primary tumor and metastases, chart their genetic drivers, and distinguish metastatic and non-metastatic subclones.

  Dataset EGAD50000000005

• IBD dataset

  We performed multi-omics profiling of 38 Crohn's disease and Ulcerative colitis patients across several stimulations (RPMI, LPS, Salmonella, in total 80 samples). Nuclei were profiled using the 10X Multiome protocol which offers paired RNA+ATAC from the same nucleus (e.g. shared barcodes). Per library, the ATAC (I1, R1, R2, R3 reads) and RNA (I1, I2, R1, R2 reads) are provided. Pools are genetically multiplexed across donors. Genotype files are provided to allow genetic demultiplexing.

  Dataset EGAD50000000198

• Non-coding mutations drive persistence of a founder pre-leukemic clone which initiates late relapse in T-ALL

  T-ALL relapse usually occurs early but can occur much later, which has been suggested to represent a de novo leukemia. However, we conclusively demonstrate late relapse can evolve from a pre-leukemic subclone harbouring a non-coding mutation that evades initial chemotherapy. Data include 19 WGS samples: - 5 cases with presentation, relapse and remission (germline) samples - 2 cases with presentation and relapse samples, but not remission (germline)

  Dataset EGAD50000000174

• Non-coding mutations drive persistence of a founder pre-leukemic clone which initiates late relapse in T-ALL

  T-ALL relapse usually occurs early but can occur much later, which has been suggested to represent a de novo leukemia. However, we conclusively demonstrate late relapse can evolve from a pre-leukemic subclone harbouring a non-coding mutation that evades initial chemotherapy.

  Study EGAS50000000129

• Small-RNA sequencing of pheochromocytoma and paraganglioma arising from germline SDHB mutations

  Single-end 75 basepair small-RNA sequencing of 90 SDHB-deficient non-metastatic and metastatic pheochromocytoma and paraganglioma. Samples were prepared using the NEXTFLEX® Small RNA-Seq Kit v3 (Bioo Scientific ). Samples were sequenced at the molecular genomics core (Peter MacCallum Cancer Centre) using 50bp single end sequencing on the Illumina NextSeq 500 (Illumina, USA). This dataset contains raw sequencing reads in FASTQ format.

  Dataset EGAD50000000501

• RNA-seq from Glioblastoma treated with Indisulam

  The dataset includes RNA-sequencing results from four patient-derived glioblastoma cell lines treated with DMSO (vehicle control) or the splicing modulating-drug indisulam (at 6 and 16 hours), resulting in 12 RNA-seq samples. Paired-end sequencing produced 24 FASTQ.gz files. The RNA libraries were prepared using PolyA selection and ERCC spike-ins and sequenced on a NovaSeq platform. This dataset supports the analysis of drug-induced transcriptomic changes and the prediction of subsequent non-canonical tumor-specific antigens (ncTSAs) using the NovumRNA pipeline.

  Dataset EGAD50000000957

• Identification of Novel Immunotherapy Targets in Myeloma

  RNA sequencing (RNA-Seq) was performed on 94 multiple myeloma (MM) patient samples. We used genomic subgroup and high-risk markers to identify therapeutic targets, including TNFRSF17, GPRC5D, ITGA4, and LAX1, with low predicted toxicity and high specificity to MM and genomic subgroups such as those with TP53 alterations.

  Study phs003772

• Epigenetic memory of SARS-CoV-2 mRNA vaccination in monocyte-derived macrophages

  Immune memory is key to effective antimicrobial responses, but the impact of mRNA vaccines on this process is not fully understood. Our research shows that SARS-CoV-2 mRNA vaccines alter the epigenetic profile of human macrophages, specifically enhancing histone acetylation, which is linked to immune training. Significant epigenetic changes, along with increased cytokine release, require two vaccine doses. However, these effects diminish over time but can be restored with a booster dose six months later, maintaining a strong pro-inflammatory response.

  Dataset EGAD50000000495

• B cell transcriptome and repertoire data from patients with IBD and healthy controls

  This dataset contains transcriptome data generated from naive and memory B cells isolated from patients with inflammatory bowel disease and healthy controls. Data was generated from both patients with Crohn's disease and ulcerative colitis. In addition, it contains BCR repertoire data from patients with IBD and healthy controls. The repertoire data was generated using amplicon sequencing of RNA isolated from peripheral blood, lymph nodes from inflamed gut and gut associated lymphatic tissue.

  Dataset EGAD50000001335

• Low-coverage Single-cell Whole Genome Sequencing Data from Paired Meningioma Samples

  This dataset comprises low-coverage (~0.5X) whole genome sequencing data from 179 single cells isolated from paired meningioma samples (88 cells from initial grade II and 91 cells from recurrent grade III tumor from the same patient). The single-cell libraries were constructed using Primary Template Amplification and ResolveDNA protocol, with libraries subsequently sequenced on NextSeq 1000 using 2x150bp paired-end reads targeting 8M reads per cell. This dataset includes the sequencing data in Fastq format.

  Dataset EGAD50000001254

• RNA-Seq of Myeloid Cells in Dendritic Cell Therapy Response

  RNA libraries were prepared from 100 ng of total RNA using the Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit, then sequenced (2×150 bp) on the Illumina NextSeq550. Transcript-level quantification was done with kallisto, followed by gene-level summarization (tximport) and differential expression analysis (DESeq2). Quality control included PCA, hierarchical clustering, and deconvolution with CIBERSORTx to exclude non-myeloid genes. Final analyses identified transcriptomic differences among healthy donors and three patient subgroups based on response to dendritic cell therapy.

  Dataset EGAD50000001681

• cfDNA sWGS BAM — Healthy donors

  Paired-end shallow whole-genome sequencing (sWGS) of plasma cfDNA from healthy donors recruited at EFS Montpellier (France). Libraries: DSP (NEBNext Ultra II) and/or SSP (IDT/Swift Accel-NGS 1S Plus). Sequencing by IntegraGen (France, 2022–2024). Reads aligned to GRCh38 (hg38 canonical) with BWA-MEM; BAMs coordinate-sorted and indexed; submission contains primary mapped reads only (unmapped/secondary/supplementary/duplicates removed; typical filter “-F 3332”, MAPQ threshold as noted in analysis records). Each BAM/BAI pair is linked to its Sample and Experiment. Data Use: controlled access.

  Dataset EGAD50000001880

• Long-read single-cell RNA-seq in COVID-19

  We report the first application of long-read single-cell RNA sequencing on nasopharyngeal swabs from COVID-19 patients and healthy controls to resolve transcript-level changes across cell types. Samples were collected from three patients with moderate COVID-19, six patients with critical COVID-19, and three healthy controls. Single-cell libraries were generated using the 10x Genomics Chromium 3' protocol, producing unfragmented cDNA. Libraries were sequenced on the Oxford Nanopore Technologies PromethION platform. Basecalling was performed with Guppy (v1.6), generating a single FASTQ file per sample.

  Dataset EGAD50000001836

• Identifying aberrant splicing isoforms and potential neoantigens in non-small cell lung cancer

  To identify aberrant splicing isoforms and potential neoantigens, we performed full-length cDNA sequencing of seven non-small cell lung cancer specimens using a long-read sequencer MinION. We detected aberrant splicing isoforms using our bioinformatics pipeline and constructed a comprehensive catalogue.

  Study JGAS000245

• NAR-GAB 2025 deposit data

  Paired-end whole-exome sequencing data derived from Illumina hybrid-capture experiments (Agilent SureSelect Human All Exon kits). Six human probands with rare diseases; one sample per subject. Sequencing reads from each individual were processed into analysis-ready gVCF files following standard best-practice pipelines, including alignment, duplicate marking, base quality calibration, and variant calling. All gVCF files are encrypted using Crypt4GH and are available under controlled access through our DAC in accordance with a strict DUO-based policy.

  Dataset EGAD50000002100

• Metagenomic data of patients with bipolar disorder or schizoprhenia spectrum disorder

  Metagenomic data of stool samples from 111 patients with either bipolar disorder or schizophrenia spectrum disorder. Data includes fq.gz files, mostly 1 forward and 1 reverse read per sample. Samples analysed in multiple lanes have 4 (paired) fastq files, which will have the same patient ID (example: 048_1 and 048_2, or 088_L1 and 088_L2. DNA was extracted from using the QIAamp Fast DNA Stool Mini Kit (Qiagen) following the manufacturer’s instructions. Shotgun metagenomic sequencing was carried out using llumina Novaseq 6000.

  Dataset EGAD50000001414

• Bell_activation_timecourse

  We purified human naive and memory B cells from PBMCs. We stimulated them with IgM cross-linker providing BCR stimulation, multimeric CD40L that engages costimulatory receptor CD40 on the B cell, and cytokines IL-2 and IL-21. To comprehensively characterise activation dynamics of naive and memory B cells, we performed single-cell RNA sequencing (scRNA-seq) and B cell receptor sequencing (BCR-seq) in resting cells (day 0), before the first division (day 1), at the time of the first division (day 3) and following the full B cell differentiation (day 6)

  Dataset EGAD50000002115

• Shallow Whole-Genome Sequencing of Plasma ctDNA in Relapsed/Refractory Germ Cell Tumors

  This dataset comprises shallow whole-genome sequencing data (~3× coverage) of circulating tumor DNA extracted from baseline and on-treatment plasma samples of patients with relapsed or refractory germ cell tumors treated with salvage high-dose chemotherapy. Libraries were generated from 20 ng of cfDNA using the KAPA Hyper Prep protocol with unique dual indexing and sequenced on an Illumina NovaSeq 6000 platform to enable genome-wide copy number and biomarker analyses associated with treatment response and clinical outcome.

  Dataset EGAD50000002183

• PHRT study of longitudinal sampling in ovarian cancer

  High-grade serous ovarian cancer presents significant challenges due to its poor prognosis and high heterogeneity, both of which complicate treatment responses. This project aims to understand intra-patient tumor evolution by investigating different sampling sites (primary and metastatic) at the time of diagnosis and during disease recurrence.

  Study EGAS50000001424

• Single nucleus mRNA sequencing of immune cells from diverse CNS regions in human health and diseases

  CNS nuclei were isolated from frozen specimen, stained with anti-NeuN and anti-Olig2, FACS purified (DAPI+NeuN-Olig2-), and analyzed with single nucleus RNA-seq. One batch of samples was also labelled with CMO and allows distinguishing indivudal samples within the analysis. A combined seurat object was generated to include all the analyses and samples were integrated using Harmony integration.

  Dataset EGAD50000001835

• Spatiotemporal genomic architecture informs precision oncology in glioblsatoma

  We characterized genomic and expression profiles across 127 multi-sector or longitudinal specimens from 52 glioma patients. We showed that, while samples from nearby geographical location shared similar genomic alterations (clonal or subclonal) and expression signatures, multifocal tumors were seeded from individual clones.

  Study EGAS00001001880

• Single cell Transcriptomic Analysis of Cellular Heterogeneity in Human Colorectal Tumors

  1,591 single cells from 11 colorectal cancer patients were profiled using Fluidigm based single cell RNA-seq protocol to characterized cellular heterogeneity of colorectal cancer. 630 single cells from 7 cell lines were profiled similarly to benchmark de novo cell type identification algorithms.

  Study EGAS00001001945

• Cancer-Associated Mutations in Endometriosis without Cancer

  Endometriosis, defined as the presence of ectopic endometrial stroma and epithelium, affects approximately 10% of reproductive-age women and can cause pelvic pain and infertility. Endometriotic lesions are considered to be benign inflammatory lesions but have cancerlike features such as local invasion and resistance to apoptosis

  Study EGAS00001003576

• Genetic heterogeneity and dynamics of transcriptional subtypes in matched primary and recurrent head and neck squamous cell carcinomas

  To get a better understanding of different HNSCC subtypes, whole-exome (matched tumor-normal paits) and whole transcriptome sequencing to to elucidate underlying molecular processes. Here, we present the matched whole-exome sequencing data from 28 patients (normal tissue, tumor tissue, relapse).

  Study EGAS00001005005

• Unravelling the contribution of HIF pathway and its therapeutic potential in human AML leukemia-initiating cells

  This study hypothesized that hypoxia contributes to AML-LSCs function and represents a potential therapeutic target to sensitize AML-LSCs to chemotherapy. We provide a comprehensive single-cell expression atlas of AML patient-matched diagnostic-relapsed samples from risk-stratified human AML patients.

  Study EGAS00001005980

• PBMC gene expression profiles in diet treated celiac disease upon oral gluten challenge

  This dataset contains PBMC genome-wide RNAseq reads from 21 samples and one expression matrix file after alignment and aggregation of the 21 samples. The samples are case-control drawn on day 6 from long-term GFD treated CD patients after 3 day oral gluten challenge, on day 0 from patient controls on long-term GFD treatment, and on day 6 from 4 week GFD treated healthy controls after 3 day oral gluten challenge.

  Dataset EGAD00001006655

• McGill Sperm Methylome Sequencing Data

  The study includes NGS-based WGBS on one sperm DNA sample pooled from 30 participants, and methylC-capture sequencing (MCC-Seq) on the same pooled sperm sample as well as 45 sperm DNA samples derived from both fertile and infertile individuals in two cohorts (Toronto, a fertile cohort; Montreal, an idiopathic infertility cohort). All the data were generated with 100bp paired-end reads using the Illumina HiSeq2000 or 4000 systems.

  Dataset EGAD00001004978

• scRNA-seq, scTCR-seq and scBCR-seq of 21 individuals post Covid'19 vaccination.

  This data includes scRNA-seq, scTCR-seq and scBCR-seq of 21 individuals post Covid'19 vaccination. Individuals range from the ages 52 to 75. Samples were genotype multiplexed in an overlapping mixture design, pooled, and sequenced on 16 lanes (10X, 5' GEM).

  Dataset EGAD00001011201

• Next Generation Sequencing Characterization of Hematopoietic Stem and Progenitors Cells in Human Systemic Lupus Eryhtematosus (2)

  This dataset contains RNA-sequencing of Bone marrow-derived CD34+ cells from Healthy Controls (n=2) and SLE patients (n=10). SLE patients are divided into two categories based on severity: patients with moderate/mild disease (n=4) and patients with severe disease (n=6). Libraries were generated using the Illumina TruSeq Sample Preparation kit v2. Single-end 75-bp mRNA sequencing was performed on Illumina NextSeq 500. The raw fastq files are uploaded.

  Dataset EGAD00001009744

• Single-cell bam files and RNA sequencing of viral RNA stocks

  244 infected single-cell alveolar bam files, 48 empty well bam files, and 52 RNA sequencing of amplicons (4 SARS-CoV-2 variants with 12 batches and 4 viral variants pool samples). 244 alveolar single cells were captured over 12 experimental batches and experimental condition is written in metadata uploaded as "infected_cells_final_revision.csv". on github (https://github.com/twkim-0510/SARS-CoV-2_viral_competition). Each bam file name corresponds to the sample_name column of the metadata.

  Dataset EGAD00001009711

• Comprehensive RNA repository of tissue and plasma from patients with esophageal cancer or precursor lesions

  A comprehensive RNA repository (both coding and non-coding) from 17 patients diagnosed with esophageal adenocarcinoma, high-grade dysplastic or non-dysplastic Barrett’s esophagus. Per patient, a blood plasma sample, and a healthy esophageal and disease tissue sample were collected. This dataset includes both mRNA and small RNA sequencing data (fastq.gz files) of all tissue and plasma samples. In total,102 RNA-seq libraries from 51 samples (17 plasma and 34 tissue samples) were sequenced (plasma mRNA libraries were sequenced twice).

  Dataset EGAD00001006857

• SNF_OLINK_20

  Matrix of normalized values from Olink assay performed on baseline BM Plasma. The Olink Immuno-Oncology multiplex proteomic Panel included 92 proteins associated with human inflammatory conditions. Data is analyzed using real-time PCR analysis software via the Ct method and Normalized Protein Expression (NPX) manager. Data were normalized using internal controls in every single sample, inter-plate controls, negative controls and a correction factor and expressed as Log2 scale, which was proportional to the protein concentration. One NPX difference equals the doubling of the protein concentration.

  Dataset EGAD00001011147

• pan-cancer plasma cfRNA

  Dataset contains mRNA capture sequencing data from plasma of 266 different human donors. The first, pan-cancer, cohort covers 25 high-grade to metastatic cancer types (8 cancer patients per type) and a control group (8 healthy donors). The validation cohort comprises additional plasma samples from ovarian, prostate and uterine cancer patients (12 per type) as well as additional samples from controls (22 new and 8 repeated). Samples were sequenced on a NovaSeq 6000 and are provided in FASTQ format.

  Dataset EGAD00001009713

• Chronic lymphocytic leukemia driven by paradoxical ERK activation during BRAF inhibitor treatment

  Whole-exome sequencing of a chronic lymphocytic leukemia (CLL) developed during vemurafenib treatment of a patient with malignant melanoma. Peripheral blood mononuclear cells were separated by Ficoll gradient centrifugation. DNA was extracted from highly purified (>97%) CD19+CD5+ cells obtained from the patient while being under BRAF inhibition versus CD14+ germline control cells (>90% purity). No alterations that could be linked to aberrant RAS activity or paradoxical RAF/MEK/ERK signaling could be identified in the CLL, which shows characteristic copy number alterations.

  Dataset EGAD00001000997

• Candidate diagnostic variants reported into DECIPHER, Wright NEJM 2023

  Candidate diagnostic variants reported into DECIPHER by 4 April 2022, annotated with clinical and automated pathogenicity assertions (see DOI: 10.1056/NEJMoa2209046). Genomic Diagnosis of Rare Pediatric Disease in the United Kingdom and Ireland, Wright et al, NEJM 2023.

  Dataset EGAD00001010137

• DCM-controls

  DCM-controls (113 human non-DCM samples) human heart biopsies from 113 non-diseased controls were subjected to RNA sequencing in order to assess transcriptome variation. We used Illumina HiSeq2000 technology. Each sample-dataset contains the output from tophat-1.4.1 (one *.bam file with the aligned reads and two *.fq files one with the not aligned forward read and one with the revers unaligned reads). We reveal extensive differences of gene expression and splicing between dilated cardiomyopathy patients and controls.

  Dataset EGAD00001003391

• DCM-cases

  DCM-cases (149 human DCM samples) human heart biopsies from 149 patients with dilated cardiomyopathy (DCM) were subjected to RNA sequencing in order to assess transcriptome variation. We used Illumina HiSeq2000 technology. Each sample-dataset contains the output from tophat-1.4.1 (one *.bam file with the aligned reads and two *.fq files one with the not aligned forward read and one with the revers unaligned reads). We reveal extensive differences of gene expression and splicing between dilated cardiomyopathy patients and controls.

  Dataset EGAD00001003390

• RNAseq from PDAC samples

  BAM files from RNA-seq of PDAC samples used in the COMPASS hENT1 study

  Dataset EGAD00001009409

• microRNA-seq of human serum from a longitudinal study of 66 women with no history of cancer

  This dataset includes microRNA sequencing data from 198 human serum samples, representing a subset of 66 women with no history of cancer who participated in the UKCTOCS study and with serum samples collected at three timepoints over a period of up to 5 years. Small RNA libraries prepared from the serum samples were sequenced with 50-bp single end reads on an Illumina HiSeq 2000 instrument. Data is provided as FASTQ files.

  Dataset EGAD00001004348

• Dataset Plasma-seq

  We performed low coverage whole genome sequencing of plasma DNA from prostate cancer patients to establish copy number profiles on both a genome-wide and a gene-specific level. The data include plasma samples from prostate cacner patients (n=13), non-malignant controls (males, n=10 and females, n=9), plasma samples from pregnancies with aneuploid and euploid fetuses (n=4). Furthermore, we sequenced different tumor samples (n=6) of one patients and a serial dilution of HT29 in a background of normal DNA (n=9).

  Dataset EGAD00001000364

• Targeted gene panel sequencing of matched diagnosis-remission-relapse B cell precursor acute lymphoblastic leukemia samples

  Bone marrow mononuclear cells from patients diagnosed with B cell precursor acute lymphoblastic leukemia were obtained at three sequential time points: first diagnosis, remission after chemotherapy and relapse. Genomic DNA was isolated and targeted gene panel sequencing was performed using a customized biotinylated RNA oligo pool (SureSelect, Agilent, Santa Clara, California) to hybridize the target regions comprising 362 kbp on a HiSeq2000. Target regions were selected to validate mutations previously identified in these samples using whole exome sequencing.

  Dataset EGAD00001004977

• Genomic Signatures Reveal DNA Damage Response Deficiency in Brain Metastases of Colorectal Cancer

  Brain metastasis (BM) of colorectal cancer (CRC) is rare but lethal and lacks effective therapies or a good understanding of its genomic landscapes. We conduct an analysis of whole-exome sequencing (WES, Illumina HiSeq 2500 sequencing platform) on 11 patient-matched BMs, primary CRC tumours, and adjacent normal tissues; and whole-genome sequencing (WGS, Illumina HiSeq X Ten platform) on 8 patient-matched BMs, primary CRC tumors, and adjacent normal tissues to uncover the whole-genome mutational landscape of colorectal cancer with brain metastasis.

  Dataset EGAD00001005030

• Next Generation Sequencing Characterization of Hematopoietic Stem and Progenitors Cells in Human Systemic Lupus Eryhtematosus

  This dataset contains RNA-sequencing of Bone marrow-derived CD34+ cells from Healthy Controls (n=2) and SLE patients (n=8). SLE patients are divided into two categories based on severity: patients with moderate/mild disease (n=3) and patients with severe disease (n=5). Libraries were generated using the Illumina TruSeq Sample Preparation kit v2. Single-end 75-bp mRNA sequencing was performed on Illumina NextSeq 500. The raw fastq files are uploaded.

  Dataset EGAD00001005052

• Reconstructed VDJ sequences from Smart-seq2 data

  The dataset contains reconstructed VDJ sequences (fasta files) and accompanying metadata for each cell (csv file) from scRNA-seq data generated with the Smart-seq2 protocol. The VDJ sequences were reconstructed with the computational tool BraCeR using raw fastq files as input. The dataset contains sequences from 355 IgA+ peripheral blood B-lineage cells of two untreated celiac disease patients. The sequences comprise both IgA+ transglutaminase 2-specific and other IgA+ B cells.

  Dataset EGAD50000000341

• EED inhibition of organoid development

  Transcriptomics and epigenomics after chemical inhibition of EED during early human brain organoid development. To investigate the role of H3K27me3 inhibition during neuroectoderm induction, we treated brain organoids with 3 concentrations of EED inhibitor (and control) during the transition of pluripotency to neuroepithelium. At the neuroepithelium stage, we profiled the organoids using scRNA-seq (transcriptome) and bulk Cut&Tag (H3K27me3, H3K27ac). Library preparation for scRNA-seq was carried out with the 10x genomics platform.

  Dataset EGAD50000000224

• RNA-sequencing from ALL patients treated on the Australasian Leukaemia and Lymphoma Group (ALLG) ALL06 study.

  Dataset contains RNA-sequencing data (fastq files) from 45 patients treated on the the Australasian Leukaemia and Lymphoma Group (ALLG) ALL06 study, an MRD-stratified Paediatric Protocol. Patient samples (bone marrow or peripheral blood) were taken at diagnosis. mRNA was extracted from blast cells and underwent paired-end sequencing (75bp) using the illumina NextSeq platform. Genomic data was used for identification of genomic drivers of acute lymphoblastic leukaemia (ALL).

  Dataset EGAD50000001111

• WGS data for Pancreatic Cancer samples (resection cohort)

  WGS data from pancreatic cancer samples. These are part of a resected cohort from a tandem duplicator phenotype paper (Farooq et al, NPJ Precision Oncology, 2025). The dataset includes tumour and normal BAM files sequenced on Illumina HiSeq/NovaSeq and aligned against GRCh38 (n=189 tumour/normal pairs).

  Dataset EGAD50000001834

• Single cell data from TB patients

  The dataset comprises single-cell RNA sequencing (scRNA-seq) data derived from around 60,000 PBMCs collected from donors across different severity groups of extrapulmonary tuberculosis (EPTB) and healthy controls (3 healthy, 3 mild, 3 intermediate, 3 severe). The data include both transcriptomic and surface protein expression profiles obtained using the BD Rhapsody Single-Cell Multiomics System. Libraries were prepared for whole transcriptome analysis (WTA), AbSeq, and sample tagging, with sequencing performed on a NovaSeq 6000 system.

  Dataset EGAD50000001118

• Tapestri Sequencing Data of PDAC Autopsy Samples

  This dataset comprises single-cell DNA sequencing data for selected pancreatic ductal adenocarcinoma (PDAC) autopsy samples. It employs a targeted gene panel to identify single nucleotide variants (SNVs) and copy number variations (CNVs) using the Mission Bio Tapestri platform. The samples encompass primary and metastatic tissue from selected PDAC patients. This dataset includes 74 sample-level BAM files and 24 patient-level H5 files, generated by the MissionBio pipeline.

  Dataset EGAD50000001936

• PHRT longitudinal ovarian cancer dataset

  High-grade serous ovarian cancer presents significant challenges due to its poor prognosis and high heterogeneity, both of which complicate treatment responses. This project aims to understand intra-patient tumor evolution by investigating different sampling sites (primary and metastatic) at the time of diagnosis and during disease recurrence. A total of 183 biopsies from 50 patients were collected for this purpose, and bulk mRNA sequencing was performed. The majority of samples originated from following tissue types: omentum, ovary, and ascites.

  Dataset EGAD50000002064

• Single-cell RNA sequencing of Small Intestinal Neuroendocrine Tumors (SI-NET)

  Single-cell RNA sequencing (scRNA-seq) was performed on cells isolated from intestinal mucosa and small intestinal neuroendocrine tumors (SI-NETs) to compare their transcriptomic profiles. Tumor and adjacent normal tissues were collected from two SI-NET patients, enzymatically dissociated, and processed into single-cell suspensions. Single-cell libraries were generated using the Chromium Single Cell 3′ Reagent Kit v3 and sequenced on an Illumina platform to produce FASTQ files for downstream analysis.

  Dataset EGAD50000002265

• Bulk RNA sequencing of 36 multi-region IPMN–PDAC tumours comprising 160 sequencing runs

  This dataset contains bulk RNA sequencing data generated from 36 multi-region tumour samples obtained from patients with intraductal papillary mucinous neoplasms (IPMN) and associated pancreatic ductal adenocarcinoma (PDAC). A total of 160 sequencing runs are included. Libraries were prepared from poly(A)-selected RNA and sequenced on an Illumina platform. The data are provided as raw sequencing files for downstream transcriptomic analyses.

  Dataset EGAD50000002215

• Raw and processed snRNAseq data of Choroid Plexus Tumors

  This dataset contains raw sequencing and processed data of single nuclei transcriptomes. The data were generated with 10x chromium probe-based single-nucleus assay on FFPE tissues of 43 Choroid Plexus Tumour resections and 12 non-neoplastic fetal and adult ChP resections. Raw data contain BAM files of the sequencing. Processed data contain count matrices as generated by 10x CellRanger for raw and filtered running options.

  Dataset EGAD50000002320

• Jeju Genome Project DAC

  This Data Access Committee (DAC) evaluates and manages access requests for large-scale genomic and phenotypic datasets generated as part of the Jeju Genome Project (JGP). The committee's mission is to facilitate responsible data sharing to advance precision medicine and population genetics. The DAC ensures that data access is granted only to bona fide researchers who agree to the terms of the Data Access Agreement (DAA) and whose proposed research is strictly consistent with the informed consent provided by the participants and the ethical guidelines of the project.

  Dac EGAC50000000938

• Cell types of the human retina and its organoids at single-cell resolution. Cowan et al

  Human organoids recapitulating the cell-type diversity and function of their target organ are valuable for basic and translational research. We developed light-sensitive human retinal organoids with multiple nuclear and synaptic layers, and functional synapses. We sequenced the RNA of 285,441 single cells from these organoids at seven developmental time points and from the periphery, fovea, pigment epithelium and choroid of light-responsive adult human retinas.

  Dataset EGAD00001006350

• Metagenomic sequences from human stool samples

  ​DNA extraction from human stool samples was performed at the Center for Microbiome Innovation (CMI) at University of California, San Diego. DNA sequencing libraries were prepared using Nextera XT (Illumina). Shotgun DNA sequencing was performed on the Illumina HiSeq4000 platform. Raw fastq reads were quality-checked. Skewer (version 0.2.2) was utilized with the paired-end mode. Human reads were identified and removed by Bowtie2 mapping against the human genome reference (hg19), followed by bam2fastq with --unaligned --no-aligned --force options.

  Dataset EGAD00001006364

• RNA-seq data

  This dataset contains 200 RNA-seq bam files (142 SLE, 58 healthy individuals). RNA libraries were prepared with the Illumina TruSeq sample preparation kit and were sequenced on Illumina HiSeq2000. 49 bp paired-end reads were mapped to the GRCh37 reference human genome using the GEM mapper.This dataset was generated as part of the following study: Panousis et al (2019). Combined genetic and transcriptome analysis of patients with SLE: Distinct, targetable signatures for susceptibility and severity

  Dataset EGAD00001005037

• Lymphocyte Gut WGS H38 (2021-02-02)

  We study lymphocyte somatic evolution through the sequencing of normal healthy lymphocytes. We perform whole-genome sequencing of single-cell derived T and B cell colonies to identify somatic mutations, and perform targeted deep-sequencing of these mutations. The lineages of T and B cells, and the frequencies of these mutations reveals the neutral and non-neutral evolutionary processes underlying lymphocyte growth and function. . This dataset contains all the data available for this study on 2021-02-02.

  Dataset EGAD00001006934

• Haplotype Reference Consortium Release 1.1

  Haplotype Reference Consortium Release 1.1 - subset for release via the EGA

  Dataset EGAD00001002729

• Low Coverage Whole Genome Sequencing from high grade osteosarcoma

  This dataset contains the WGS of 35 samples (high grade osteosarcoma). All cases were reviewed by an expert bone pathologist and have a tumour content of 50% minimum. Paired-end libraries from fresh frozen tumour samples were prepared using the Agilent SureSelectXT HumanV5 kit for whole-genome sequencing (WGS). These were sequenced together with a tumour complementary DNA on an Illumina HiSeq2500 (paired-end 100 bp). Sequencing reads were mapped to the GRCh37 human reference genome using HISAT2

  Dataset EGAD00001006540

• McGill EMC Community projects Release 7 for cell line "lung epithelial"

  Complete reference epigenome (as defined by IHEC) of a lung epithelial cell line with non-small Cell Lung Adenocarcinoma

  Dataset EGAD00001007679

• Whole genome sequencing of multifocal ileal neuroendocrine tumors

  This dataset includes whole genome sequences of 75 synchronous primary tumors, 15 metastases, and corresponding normal samples from 13 patients with multifocal ileal neuroendocrine tumors. The whole genomes were sequenced on Illumina HiSeq X Ten to generate 151-bp paired-end reads, which were aligned to GRCh38/hg38 reference assembly using BWA–MEM and duplicate-marked with Picard tools. GATK was utilized for base score recalibration and local indel re-alignments. The whole genomes are provided as CRAM files.

  Dataset EGAD00001008831

• BLUEPRINT September 2016, ChIPmentation T-cell Acute Lymphocytic Leukemia from capillary blood, on Genome GRCh38

  ChIPmentation data for 2 sample(s) T-cell Acute Lymphocytic Leukemia from capillary blood, on Genome GRCh38. 2 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT (September 2016).

  Dataset EGAD00001002938

• BLUEPRINT September 2016, RNA-Seq Acute Lymphocytic Leukemia from bone marrow, on Genome GRCh38

  RNA-Seq data for 1 sample(s) Acute Lymphocytic Leukemia from bone marrow, on Genome GRCh38. 1 run(s), 1 experiment(s), 0 alignment(s). Part of BLUEPRINT (September 2016).Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811

  Dataset EGAD00001002954

• BLUEPRINT September 2016, RNA-Seq Acute Myeloid Leukemia from venous blood, on Genome GRCh38

  RNA-Seq data for 1 sample(s) Acute Myeloid Leukemia from venous blood, on Genome GRCh38. 1 run(s), 1 experiment(s), 0 alignment(s). Part of BLUEPRINT (September 2016).Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811

  Dataset EGAD00001002958

• Cancer gene panel (T200.1) sequencing analysis of adult type ovarian granulosa cell tumors (Validation cohort from Hillman, et al)

  Cancer gene panel (T200.1) sequencing data from tumor/normal pairs for adult type ovarian granulosa cell tumor sequencing project. This data set contains 55 tumor panel sequencing data and 44 matched normal panel sequencing data generated using the MD Anderson Cancer Center T200.1 cancer gene hybrid capture platform, with sequencing performed on an Illumina HiSeq 2000. This dataset contains BAM files generated by aligning paired-end reads to the hg19 reference genome.

  Dataset EGAD00001004091