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• APCDR AGV Project: Low depth (4x) Illumina HiSeq sequence data for a Zulu population(BAMs)

  Low depth (4x) Illumina HiSeq raw sequence data for 100 unrelated Zulu from Durban area, South Africa.

  Dataset EGAD00001001007

• Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma

  Sequence reads for pediatric GBM samples for manuscript: Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma

  Dataset EGAD00001000134

• Sequencing data for Australian Ovarian Cancer study submitted 20121116

  Sequencing data for Australian Ovarian Cancer study submitted 20121116

  Dataset EGAD00001000293

• scRNAseq of ARID1B+/+ (control) and ARID1B+/- human telencephalic organoids at D120

  This dataset contains scRNAseq data of human telencephalic organoids, at day 120, from 4 different sequencing runs (libraries), as follows (please see cell line clone nomenclature in original publication): 1. Library 177136: Pat.2 ARID1B+/+ clone 2c (2 organoids, E11rep_1, E11rep_2), Pat.2 ARID1B+/- clone 2a (2 organoids: B002orig_1, B002orig_2) 2. Library 178119: Pat.2 ARID1B+/+ clone 2c (3 organoids: E11rep_1, E11rep_2, E11rep_3), Pat.2 ARID1B+/- clone 2a (3 organoids: B002orig_1, B002orig_2, B002orig_3) 3. Library 178120: Pat.2 ARID1B+/+ clone 2d (3 organoids: A3rep_1, A3rep_2, A3rep_3), Pat.2 ARID1B+/- clone 2b (3 organoids: B002_F7_1, B002_F7_2, B002_F7_3) 4. Library 184337: Pat.1 ARID1B+/- clone 1a (3 organoids: B001orig_1, B001orig_2, B001orig_3), HD.1 ARID1B+/+ clone 3a (3 organoids: 176_1, 176_2, 176_3), HD.1 ARID1B+/- clone 3b (3 organoids: F10_1, F10_2, F10_3)

  Dataset EGAD50000000498

• EASI-Genomics GM21886 Cell Line High Molecular Weight DNA Sequencing

  An interlaboratory study was performed with GM21886 cells to evaluate methods for high molecular weight (HMW) genomic DNA extraction and compare sample and sequencing QC metrics, and pipelines for structural variant (SV) calling. Four laboratories prepared HMW genomic DNA using four alternative extraction methods FireMonkey (Revolugen), Genomic Tip (QIAGEN), Nanobind (Circulomics), and Puregene (QIAGEN), followed by Short Read Elimination (Circulomics) and long-read sequencing with MinION and PromethION flowcells (Oxford Nanopore Technologies).

  Study phs003958

• Comprehensive biomarker analysis from phase II study of nivolumab in patients with thymic carcinoma

  In a phase II trial of nivolumab in advanced thymic carcinoma (UMIN000022007), long SD (SD for more than 24 weeks) was seen in three patients and irAE (Gr2 or higher) was seen in four patients among 15 patients. We conducted preplanned comprehensive biomarker analyses. We obtained whole blood for Immuno Pharmacogenomic analysis using PBMC DNA. Immuno-PGx analysis showed non-synonymous SNVs in ITGAX and PDCD1 had some correlation with PFS.

  Study JGAS000588

• International consensus definition of DNA methylation subgroups in juvenile myelomonocytic leukemia

  Known clinical and genetic markers have limitations in predicting disease course and outcome in juvenile myelomonocytic leukemia (JMML). DNA methylation (DNAme) patterns in JMML have correlated with outcome across multiple studies, suggesting it as a biomarker to improve patient stratification. However, standardized approaches to classify JMML based on DNAme patterns are lacking. We therefore sought to define an international consensus for DNAme subgroups in JMML and develop classification methods for clinical implementation.

  Study EGAS00001004682

• SPEN loss drives extra-follicular diffuse large B cell lymphoma with female-specific lethality and TLR pathway therapeutic vulnerabilities

  Multiome (ATAC and GEX) sequencing for one rLN sample and one DLBCL sample

  Study EGAS50000001594

• cell-free Methylated DNA by Immunoprecipitation and Sequencing (cfMeDIP) of human meningioma samples.

  Raw data for cell-free Methylated DNA by Immunoprecipitation and Sequencing (cfMeDIP) of human meningioma samples.

  Study EGAS50000001539

• PCA Atlas donor genotyping arrays (Axiom UK Biobank v2.0)

  Raw Axiom v2.0 UK Biobank Array CEL files for PCA Atlas donor buffy-coat DNA, used to generate SNP genotypes for demultiplexing single-cell and spatial transcriptomics libraries.

  Dataset EGAD00010002818

• RNAseq for Patients of NIBIT-M4 clinical trial

  RNAseq for Patients of NIBIT-M4 clinical trial

  Dataset EGAD00001009702

• Tumour sample for patient SA998

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA998

  Dataset EGAD00001009674

• Tumour sample for patient SA1058

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA1058

  Dataset EGAD00001009673

• Normal sample for patient SA1058

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA1058

  Dataset EGAD00001009672

• A molecular signature for IL-10-producing Th1 cells in protozoan parasitic diseases

  A molecular signature for IL-10-producing Th1 cells in protozoan parasitic diseases

  Dataset EGAD00001007532

• ATAC data for Glioblastoma (EGAS00001003953, H016)

  ATAC-seq data for 2 glioblastoma cell lines (LN229, ZH487), NT and SOX10KD.

  Dataset EGAD00001006544

• Whole genome sequencing of AML samples at presentation, remission, and relapse

  Whole genome sequencing of AML blood or bone marrow at presentation and remission for 5 patients. Relapse samples are included for 2 patients, totaling 12 WGS BAM files.

  Dataset EGAD00001005120

• Chip-exo and Chip-nexus for five TFs in three colorectal cancer cell lines

  Chip-exo and Chip-nexus for FOXA1, HNF4A, KLF5, MYC, and TCF7L2 in colorectal cancer cell lines LoVo, GP5D, COLO320DM

  Dataset EGAD00001004099

• DATA FILES FOR SJOS-WGS-2ndBatch

  DATA FILES FOR SJOS-WGS-2ndBatch

  Dataset EGAD00001001053

• McGill EMC Release 4 in tissue "venous blood" for cell type "CD4-positive, alpha-beta T cell"

  McGill EMC Release 4 in tissue "venous blood" for cell type "CD4-positive, alpha-beta T cell"

  Dataset EGAD00001001280

• WGS DATA FILES FOR SJPhLike

  WGS DATA FILES FOR SJPhLike

  Dataset EGAD00001000976

• Integrative understanding of human immune system by functional genomics and development of intervention strategies for the prevention of autoimmune diseases

  Various peripheral blood immune cell subsets from 89 healthy volunteers and 136 systemic lupus erhythematosus (SLE) donors were collected (Naive_CD4, Mem_CD4, Th1, Th2, Th17, Tfh, Fr._I_nTreg, Fr._II_eTreg, Fr._III_T, Naive_CD8, EM_CD8, CM_CD8, TEMRA_CD8, NK, Naive_B, USM_B, SM_B, DN_B, Plasmablast, CL_Mono (or CD16n_Mono), CD16p_Mono, Int_Mono, NC_Mono, mDC, pDC, Neu, LDG). 22 SLE donors were analyzed longitudinally. RNA-seq was performed with each immune cell subset samples. After gene expression quantification samples were filtered.

  Study JGAS000486

• Progressive supranuclear palsy - bulk RNA seq of prefrontal cortex

  Dataset corresponding to the bulk RNA-seq dataset from prefrontal cortex for a total of N=42 samples. Tissue samples correspond to donors with pathologically confirmed progressive supranuclear palsy. RNA-seq was carried out using ribosomal depletion. Dataset contains paired fastq files, sample metadata and downstream quantification files. Quantification was performed with salmon v1.3.0 with Gencode 35 (GRCh38.p13).

  Dataset EGAD50000002623

• Multiple system atrophy - bulk RNA seq of prefrontal cortex

  Dataset corresponding to the bulk RNA-seq dataset from prefrontal cortex for a total of N=35 samples. Tissue samples correspond to donors with pathologically confirmed multiple system atrophy. RNA-seq was carried out using ribosomal depletion. Dataset contains paired fastq files, sample metadata and downstream quantification files. Quantification was performed with salmon v1.3.0 with Gencode 35 (GRCh38.p13). N=6 samples are overlapping with EGAS50000000301.

  Dataset EGAD50000002624

• Alzheimer's disease - bulk RNA seq of prefrontal cortex

  Dataset corresponding to the bulk RNA-seq dataset from prefrontal cortex for a total of N=72 samples. Tissue samples correspond to donors with pathologically confirmed Alzheimer's disease. RNA-seq was carried out using ribosomal depletion. Dataset contains paired fastq files, sample metadata and downstream quantification files. Quantification was performed with salmon v1.3.0 with Gencode 35 (GRCh38.p13).

  Dataset EGAD50000002625

• Dementia with Lewy bodies - bulk RNA seq of prefrontal cortex

  Dataset corresponding to the bulk RNA-seq dataset from prefrontal cortex for a total of N=80 samples. Tissue samples correspond to donors with pathologically confirmed dementia with Lewy bodies. RNA-seq was carried out using ribosomal depletion. Dataset contains paired fastq files, sample metadata and downstream quantification files. Quantification was performed with salmon v1.3.0 with Gencode 35 (GRCh38.p13).

  Dataset EGAD50000002626

• Parkinson's disease - bulk RNA seq of prefrontal cortex

  Dataset corresponding to the bulk RNA-seq dataset from prefrontal cortex for a total of N=448 samples. Tissue samples correspond to donors with pathologically confirmed Parkinson's disease. RNA-seq was carried out using ribosomal depletion. Dataset contains paired fastq files, sample metadata and downstream quantification files. Quantification was performed with salmon v1.3.0 with Gencode 35 (GRCh38.p13). N=81 samples are overlapping with EGAS50000000301.

  Dataset EGAD50000002627

• Controls - bulk RNA seq of prefrontal cortex

  Dataset corresponding to the bulk RNA-seq dataset from prefrontal cortex for a total of N=283 samples. Tissue samples correspond to health control donors. RNA-seq was carried out using ribosomal depletion. Dataset contains paired fastq files, sample metadata and downstream quantification files. Quantification was performed with salmon v1.3.0 with Gencode 35 (GRCh38.p13). N=21 samples are overlapping with EGAS50000000301.

  Dataset EGAD50000002628

• Corticobasal degeneration - bulk RNA seq of prefrontal cortex

  Dataset corresponding to the bulk RNA-seq dataset from prefrontal cortex for a total of N=17 samples. Tissue samples correspond to donors with pathologically confirmed corticobasal degeneration. RNA-seq was carried out using ribosomal depletion. Dataset contains paired fastq files, sample metadata and downstream quantification files. Quantification was performed with salmon v1.3.0 with Gencode 35 (GRCh38.p13).

  Dataset EGAD50000002629

• EGAD00010000744

  Subset 2 of osteoarthritis cases genotyped on Illumina 610k from the arcOGEN Consortium (http://www.arcogen.org.uk/) with consent for osteoarthritis studies only.

  Dataset EGAD00010000744

• Dataset for urologic_cancer-EXON

  Rare cancer sequencing data of 112 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008904

• Dataset for neuroendocrine_adrenal_tumor-WHOLE_GENOME

  Rare cancer sequencing data of 112 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008893

• Dataset for hepatopancreaticobiliary_malignancy-WHOLE_GENOME

  Rare cancer sequencing data of 83 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008884

• Dataset for hepatopancreaticobiliary_malignancy-EXON

  Rare cancer sequencing data of 162 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008883

• Dataset for head_and_neck_cancer-EXON

  Rare cancer sequencing data of 86 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008880

• Methylation and nucleosome occupancy studies on cell-free DNA using enzymatic cytosine conversion

  Raw sequencing data (PE, fastq.gz) from NovaSeq 6000 sequencing runs of: 1. Blood-derived cell-free DNA from six healthy controls, enzymatic cytosine conversion (between 1 and 3 replicates each) 2. Urine-derived cell-free DNA from three healthy controls, enzymatic cytosine conversion (between 1 and 3 replicates each) 3. Blood-derived cell-free DNA from six patients with acute or chronic kidney disease with/without other relevant organ dysfunction, enzymatic cytosine conversion (between 1 and 3 replicates each) 4. Urine-derived cell-free DNA from three patients with acute kidney disease, enzymatic cytosine conversion (between 1 and 3 replicates each) 5. Blood-derived cell-free DNA from three healthy controls, bisulfite cytosine conversion (single datasets) 6. Conventional whole-genome sequencing on genomic DNA of two healthy kidney donors for two of the studied patients (single datasets).

  Dataset EGAD00001006072

• Constit Genome Sequencing

  WGS blood data (fastq raw read sequences) for French ICGC leiomyosarcoma cancer sequencing project, 67 samples representing 67 donors. Sequencing was performed on Illumina HiSeq. The libraries were then sequenced with a 2 x 100bp paired-end protocol to a minimum mean coverage of 30x.

  Dataset EGAD00001003190

• Leiomyosarcoma Cancer Genome Sequencing

  WGS cancer data (fastq raw read sequences) for French ICGC leiomyosarcoma cancer sequencing project, 78 samples representing 67 donors. Sequencing was performed on Illumina HiSeq. The libraries were then sequenced with a 2 x 100bp paired-end protocol to a minimum mean coverage of 50x.

  Dataset EGAD00001003191

• WGS files for Genomic Landscape ALL paper

  WGS files for Genomic Landscape ALL paper titled "The genomic landscape of pediatric acute lymphoblastic leukemia"

  Dataset EGAD00001008600

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

  RNA-Seq data for 2 sample(s) Acute Myeloid Leukemia for myeloid cell from venous blood, on Genome GRCh38. 2 run(s), 2 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 EGAD00001002968

• BLUEPRINT September 2016, RNA-Seq for monocyte T=6day_RANK_M-CSF from venous blood, on Genome GRCh38

  RNA-Seq data for 1 sample(s) for monocyte T=6day_RANK_M-CSF 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 EGAD00001002967

• BLUEPRINT September 2016, RNA-Seq for monocyte T=10day_RANK_M-CSF from venous blood, on Genome GRCh38

  RNA-Seq data for 1 sample(s) for monocyte T=10day_RANK_M-CSF 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 EGAD00001002966

• BLUEPRINT September 2016, RNA-Seq for monocyte T=2day_S100A9_RANKL_M-CSF from venous blood, on Genome GRCh38

  RNA-Seq data for 1 sample(s) for monocyte T=2day_S100A9_RANKL_M-CSF 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 EGAD00001002965

• BLUEPRINT September 2016, RNA-Seq for monocyte T=1day_4hr_RANK from venous blood, on Genome GRCh38

  RNA-Seq data for 1 sample(s) for monocyte T=1day_4hr_RANK 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 EGAD00001002964

• BLUEPRINT September 2016, RNA-Seq Acute Lymphocytic Leukemia for precursor B cell from venous blood, on Genome GRCh38

  RNA-Seq data for 6 sample(s) Acute Lymphocytic Leukemia for precursor B cell from venous blood, on Genome GRCh38. 6 run(s), 6 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 EGAD00001002963

• BLUEPRINT September 2016, RNA-Seq Acute Myeloid Leukemia for blast cell from bone marrow, on Genome GRCh38

  RNA-Seq data for 1 sample(s) Acute Myeloid Leukemia for blast cell 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 EGAD00001002962

• BLUEPRINT September 2016, RNA-Seq for monocyte T=10day_S100A9_RANKL_M-CSF from venous blood, on Genome GRCh38

  RNA-Seq data for 1 sample(s) for monocyte T=10day_S100A9_RANKL_M-CSF 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 EGAD00001002961

• BLUEPRINT September 2016, RNA-Seq for monocyte T=6day_S100A9_RANKL_M-CSF from venous blood, on Genome GRCh38

  RNA-Seq data for 1 sample(s) for monocyte T=6day_S100A9_RANKL_M-CSF 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 EGAD00001002960

• BLUEPRINT September 2016, RNA-Seq for monocyte T=1day_M-CSF_S100A9_4hr_RANL from venous blood, on Genome GRCh38

  RNA-Seq data for 1 sample(s) for monocyte T=1day_M-CSF_S100A9_4hr_RANL 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 EGAD00001002959

• BLUEPRINT September 2016, RNA-Seq for monocyte T=2day_RANK_M-CSF from venous blood, on Genome GRCh38

  RNA-Seq data for 1 sample(s) for monocyte T=2day_RANK_M-CSF 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 EGAD00001002957