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• RNA004 Nanopore DRS of peripheral blood

  Direct RNA Sequencing offers the capability of standard transcriptomic analyses + RNA modification analysis, which holds promising applications for future clinical workflows. To this end, we tested the newly available RNA004 kit from ONT on human peripheral blood and provide orthogonal GLORI and IVT measurement for benchmarking of m6A-detection. The samples are from peripheral blood of a healthy control, taken at three different timepoints.

  Dataset EGAD50000001710

• WGS data for ctDNA monitoring for NSCLC in TRACERx

  Ultrasensitive circulating tumour DNA (ctDNA) detection can stratify clinical risk in early-stage non-small cell lung cancer (NSCLC). Here, we applied a whole-genome, tumour-informed approach to study ctDNA in more than 400 NSCLC of the TRACERx project

  Study EGAS50000001187

• Comprehensive molecular profiling with whole-exome sequencing (WES) of PDX tumors

  To identify biomarkers for the antitumor effects of molecularly targeted therapy, we performed whole-exome sequencing on 795 patient-derived xenograft (PDX) samples established from 269 patients with solid tumors and 125 frozen tissue samples obtained at the time of surgery.

  Study JGAS000853

• Molecular profiling of HGBCL-DH-BCL2 patients treated in the HOVON-152 trial

  Using targeted sequencing and shallow whole genome sequencing for simultaneous screening of mutations, copy number alterations, and translocations, this study aims to identify genomic alterations associated with outcome in HGBCL-DH-BCL2 patients of the HOVON-152 trial.

  Study EGAS50000001453

• single cell RNA sequencing and ATAC sequencing, and Whole Genome sequencing of ALS patients

  To investigate ALS pathology at the cellular level, we conducted a multiome (single-nucleus RNA sequencing and assay for transposase-accessible chromatin using sequencing) analysis using the motor cortex and spinal cord of patients with ALS and control individuals.

  Study JGAS000852

• WTCCC2 Reading and Mathematics (RM) samples

  A WTCCC2 project genome-wide association study for reading and mathematics ability in 3665 12-year-old individuals from the UK, genotyped on the Affymetrix 6.0 array. Details of the WTCCC2 analysis can be found in Davis et al. [Nat. Commun. 2014 July;5:4204]

  Study EGAS00001000886

• ERBB2/HER2 transmembrane and juxtamembrane domain mutations in cancer

  In this study, we identified several recurrent activating HER2 somatic mutations in transmembrane and juxtamembrane domain in multiple cancers and demonstrate that patients carryingthese mutations are candidates for anti-HER2 therapy. We have also identified a germline mutation in HER2 transmembrane domain.

  Study EGAS00001003213

• Warm_Autopsy_Single_Cell_X10

  Study of cell lineage and embryogenesis using biopsy samples from sites across the whole body (post mortem). Sample donors are recruited sensitively through the Phoenix study and consent to samples being taken after their death for both the Phoenix study and this WTSI study.

  Study EGAS00001001698

• Whole exome sequencing of Finnish hereditary breast cancer families

  A remarkable proportion of factors causing genetic predisposition to breast cancer (BC) are unknown in non-BRCA1/2 families. Exome sequencing was performed for 13 high-risk Finnish hereditary breast and/or ovarian cancer (HBOC) families to detect variants contributing to BC susceptibility

  Study EGAS00001001835

• The_contribution_of_POT1_variants_to_sporadic_melanoma_development

  A case-control series of melanoma cases from Leeds, UK have been sequenced in the Fluidigm platform to identify genetic variants associated with sporadic melanoma development. Samples in which potentially contributing variants have been detected are being sequenced in an orthogonal platform for variant confirmation.

  Study EGAS00001001964

• Advanced molecular neuropathology to increase diagnostic accuracy in pediatric neurooncology

  To assess their utility in routine neuropathology, we prospectively integrated DNA methylation-based CNS tumor classification and targeted gene panel sequencing of tumor and constitutional DNA with blinded neuropathological reference diagnostics for a population-based cohort of > 1,200 newly-diagnosed pediatric patients.

  Study EGAS00001006680

• Systematic analysis of paralogous regions in 41,755 exomes uncovers clinically relevant variation

  As part of the study "Systematic analysis of paralogous regions in 41,755 exomes uncovers clinically relevant variation" we wanted to identiffy the SNVs that are located in STRC and which ones in STRCP1. For this we applied targeted long-read sequencing.

  Study EGAS00001007513

• BLUEPRINT release August 2016, Bisulfite-Seq for class switched memory B cell, on genome GRCh38

  Bisulfite-Seq data for 3 class switched memory B cell sample(s). 43 run(s), 4 experiment(s), 6 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816

  Dataset EGAD00001002354

• BLUEPRINT release August 2016, ChIP-Seq for monocyte - RPMI_T=6days, on genome GRCh38

  ChIP-Seq data for 3 monocyte - RPMI_T=6days sample(s). 10 run(s), 7 experiment(s), 7 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002413

• BLUEPRINT release August 2016, ChIP-Seq for Acute Myeloid Leukemia - SAHA, on genome GRCh38

  ChIP-Seq data for 3 Acute Myeloid Leukemia - SAHA sample(s). 14 run(s), 14 experiment(s), 14 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002292

• BLUEPRINT release August 2016, ChIP-Seq for Acute Myeloid Leukemia - CTR, on genome GRCh38

  ChIP-Seq data for 7 Acute Myeloid Leukemia - CTR sample(s). 45 run(s), 44 experiment(s), 44 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002340

• BLUEPRINT release August 2016, RNA-Seq for Acute Myeloid Leukemia - SAHA, on genome GRCh38

  RNA-Seq data for 2 Acute Myeloid Leukemia - SAHA sample(s). 2 run(s), 2 experiment(s), 2 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816

  Dataset EGAD00001002343

• BLUEPRINT release August 2016, RNA-Seq for Acute Promyelocytic Leukemia - MC2884, on genome GRCh38

  RNA-Seq data for 1 Acute Promyelocytic Leukemia - MC2884 sample(s). 1 run(s), 1 experiment(s), 1 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816

  Dataset EGAD00001002352

• BLUEPRINT release August 2016, ChIP-Seq for erythroblast, on genome GRCh38

  ChIP-Seq data for 2 erythroblast sample(s). 14 run(s), 14 experiment(s), 14 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002377

• BLUEPRINT release August 2016, ChIP-Seq for Acute Myeloid Leukemia, on genome GRCh38

  ChIP-Seq data for 38 Acute Myeloid Leukemia sample(s). 244 run(s), 226 experiment(s), 226 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002418

• BLUEPRINT release August 2016, RNA-Seq for T-cell Prolymphocytic Leukemia, on genome GRCh38

  RNA-Seq data for 3 T-cell Prolymphocytic Leukemia sample(s). 3 run(s), 3 experiment(s), 3 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816

  Dataset EGAD00001002426

• BLUEPRINT release August 2016, ChIP-Seq for osteoclast, on genome GRCh38

  ChIP-Seq data for 2 osteoclast sample(s). 17 run(s), 14 experiment(s), 14 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002391

• BLUEPRINT release August 2016, Bisulfite-Seq for germinal center B cell, on genome GRCh38

  Bisulfite-Seq data for 3 germinal center B cell sample(s). 37 run(s), 4 experiment(s), 6 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816

  Dataset EGAD00001002511

• BLUEPRINT release August 2016, Bisulfite-Seq for effector memory CD8-positive, alpha-beta T cell, on genome GRCh38

  Bisulfite-Seq data for 2 effector memory CD8-positive, alpha-beta T cell sample(s). 30 run(s), 3 experiment(s), 4 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816

  Dataset EGAD00001002383

• BLUEPRINT release August 2016, Bisulfite-Seq for effector memory CD4-positive, alpha-beta T cell, on genome GRCh38

  Bisulfite-Seq data for 2 effector memory CD4-positive, alpha-beta T cell sample(s). 34 run(s), 3 experiment(s), 4 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816

  Dataset EGAD00001002367

• BLUEPRINT release August 2016, ChIP-Seq for Acute Promyelocytic Leukemia - MS275, on genome GRCh38

  ChIP-Seq data for 1 Acute Promyelocytic Leukemia - MS275 sample(s). 7 run(s), 7 experiment(s), 7 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002342

• BLUEPRINT release January 2015, RNA-Seq for regulatory T cell

  RNA-Seq data for 1 regulatory T cell sample(s). 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811

  Dataset EGAD00001001174

• BLUEPRINT release August 2016, ChIP-Seq for T-cell Acute Lymphocytic Leukemia, on genome GRCh38

  ChIP-Seq data for 9 T-cell Acute Lymphocytic Leukemia sample(s). 41 run(s), 41 experiment(s), 41 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002400

• BLUEPRINT release August 2016, ChIP-Seq for Acute Promyelocytic Leukemia - MC2392, on genome GRCh38

  ChIP-Seq data for 2 Acute Promyelocytic Leukemia - MC2392 sample(s). 14 run(s), 12 experiment(s), 12 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002406

• BLUEPRINT release August 2016, Bisulfite-Seq for mature neutrophil - G-CSF/Dex. Treatment (16-20 hrs), on genome GRCh38

  Bisulfite-Seq data for 3 mature neutrophil - G-CSF/Dex. Treatment (16-20 hrs) sample(s). 33 run(s), 3 experiment(s), 6 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816

  Dataset EGAD00001002412

• BLUEPRINT release August 2016, Bisulfite-Seq for CD4-positive, alpha-beta T cell, on genome GRCh38

  Bisulfite-Seq data for 8 CD4-positive, alpha-beta T cell sample(s). 108 run(s), 8 experiment(s), 16 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816

  Dataset EGAD00001002460

• BLUEPRINT release August 2016, RNA-Seq for Acute Promyelocytic Leukemia - MC2884 (24h), on genome GRCh38

  RNA-Seq data for 1 Acute Promyelocytic Leukemia - MC2884 (24h) sample(s). 1 run(s), 1 experiment(s), 1 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816

  Dataset EGAD00001002461

• BLUEPRINT release August 2016, ChIP-Seq for Acute Promyelocytic Leukemia - CTR, on genome GRCh38

  ChIP-Seq data for 3 Acute Promyelocytic Leukemia - CTR sample(s). 22 run(s), 21 experiment(s), 21 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002490

• BLUEPRINT release August 2015, RNA-Seq for neutrophilic metamyelocyte, on genome GRCh38

  RNA-Seq data for 2 neutrophilic metamyelocyte sample(s). 2 run(s), 2 experiment(s), 2 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820

  Dataset EGAD00001001566

• BLUEPRINT release August 2016, ChIP-Seq for monocyte - RPMI_T=4hrs, on genome GRCh38

  ChIP-Seq data for 3 monocyte - RPMI_T=4hrs sample(s). 8 run(s), 8 experiment(s), 8 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002328

• BLUEPRINT release August 2016, RNA-Seq for Acute Promyelocytic Leukemia - CTR, on genome GRCh38

  RNA-Seq data for 3 Acute Promyelocytic Leukemia - CTR sample(s). 3 run(s), 3 experiment(s), 3 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816

  Dataset EGAD00001002353

• BLUEPRINT release August 2016, RNA-Seq for neutrophilic metamyelocyte, on genome GRCh38

  RNA-Seq data for 3 neutrophilic metamyelocyte sample(s). 3 run(s), 3 experiment(s), 3 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816

  Dataset EGAD00001002366

• BLUEPRINT release August 2016, ChIP-Seq for Acute Promyelocytic Leukemia - MC2494, on genome GRCh38

  ChIP-Seq data for 1 Acute Promyelocytic Leukemia - MC2494 sample(s). 2 run(s), 1 experiment(s), 1 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002516

• Processed bam files for the whole exome sequencing of primary lung adenocarcinoma samples

  We performed single cell RNA sequencing (scRNA-seq) for 208,506 cells derived from 58 lung adenocarcinomas from 44 patients, which covers primary tumour, lymph node and brain metastases, and pleural effusion in addition to normal lung tissues and lymph nodes. The extensive single cell profiles depicted a complex cellular atlas and dynamics during lung adenocarcinoma progression which includes cancer, stromal, and immune cells in the surrounding tumor microenvironments.

  Dataset EGAD00001010320

• BLUEPRINT release August 2015, ChIP-Seq for Chronic lymphocytic leukemia, on genome GRCh38

  ChIP-Seq data for 5 Chronic lymphocytic leukemia sample(s). 24 run(s), 23 experiment(s), 23 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820

  Dataset EGAD00001001562

• BLUEPRINT release January 2015, ChIP-Seq for mature neutrophil

  ChIP-Seq data for 7 mature neutrophil sample(s). 78 run(s), 60 experiment(s), 60 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811

  Dataset EGAD00001001149

• BLUEPRINT release August 2015, ChIP-Seq for Acute Myeloid Leukemia - SAHA, on genome GRCh38

  ChIP-Seq data for 3 Acute Myeloid Leukemia - SAHA sample(s). 11 run(s), 11 experiment(s), 11 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820

  Dataset EGAD00001001485

• BLUEPRINT release August 2014, ChIP-Seq for alternatively activated macrophage

  ChIP-Seq data for 4 alternatively activated macrophage sample(s). 29 run(s), 28 experiment(s), 28 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811

  Dataset EGAD00001000938

• BLUEPRINT release August 2015, Bisulfite-Seq for endothelial cell of umbilical vein (resting), on genome GRCh38

  Bisulfite-Seq data for 2 endothelial cell of umbilical vein (resting) sample(s). 2 run(s), 2 experiment(s), 2 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_bisulphite_analysis_CNAG_20150820

  Dataset EGAD00001001486

• scRNA-seq of relapsed/refractory multipe myeloma with 10x Chromium (3´ v2)

  This dataset includes 87 scRNA-seq samples of bone marrow aspirates of 20 relapsed/refractory patients generated with the 3´(v2) kit of the 10x Chromium platform. Bone marrow cells have been sorted using CD138 +/- fractions using magnetic beads for plasma cell enrichment and processed independently. For 14/20 patients multiple treatment timepoints are available that includes samples before treatment and at relapse during treatment.

  Dataset EGAD00001006903

• BLUEPRINT release August 2016, ChIP-Seq for Acute Promyelocytic Leukemia - SAHA, on genome GRCh38

  ChIP-Seq data for 1 Acute Promyelocytic Leukemia - SAHA sample(s). 1 run(s), 1 experiment(s), 1 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002298

• BLUEPRINT release August 2016, ChIP-Seq for Acute Promyelocytic Leukemia, on genome GRCh38

  ChIP-Seq data for 1 Acute Promyelocytic Leukemia sample(s). 7 run(s), 7 experiment(s), 7 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002304

• BLUEPRINT release August 2016, ChIP-Seq for Acute Promyelocytic Leukemia - ATRA, on genome GRCh38

  ChIP-Seq data for 3 Acute Promyelocytic Leukemia - ATRA sample(s). 21 run(s), 20 experiment(s), 20 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002319

• BLUEPRINT release August 2014, RNA-Seq for mature neutrophil

  RNA-Seq data for 7 mature neutrophil sample(s). 7 run(s), 7 experiment(s), 7 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811

  Dataset EGAD00001000904

• BLUEPRINT release August 2016, RNA-Seq for Mantle Cell Lymphoma, on genome GRCh38

  RNA-Seq data for 5 Mantle Cell Lymphoma sample(s). 5 run(s), 5 experiment(s), 5 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816

  Dataset EGAD00001002336