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• BCL11B Enhancer Hijacking by t(14;16)(q32;q24) Translocation Defines a Novel High-Risk Subtype of T-ALL

  We performed integrated analysis of pediatric and adult T-ALL and mixed phenotype acute leukemias (MPALs) by whole-genome and whole-transcriptome sequencing.

  Study EGAS50000001254

• Endogenous CD4+ T Cells Recognize Neoantigens in Lung Cancer Patients, including KRAS and ERBB2 (Her2) Driver Mutations

  Neoantigen-specific T cell responses were characterized in 4 patients with non-small cell lung cancer. Candidate neoantigens were identified by sequencing tumor and normal DNA from each patient, and ranking single nucleotide variants by expression. Multiple T cell responses were isolated, and in two patients with lung adenocarcinoma, CD4+ T cell responses to recurrent oncogenic mutations in KRAS and Her2 were identified.

  Study phs001805

• Whole genome and exome sequencing data of invasive micropapillary carcinoma of breast

  This study contains whole genome sequencing data, whole exon sequencing data and mutation files of IMPC tumor and normal tissue sample.

  Study EGAS00001005902

• Matched tissue from BRCA1/2 mutation carriers and confirmed non-BRCA mutation carriers

  Methylation data from individuals with BRCA1/2 mutation and controls from cervical, buccal, and blood samples.

  Study EGAS00001005626

• Genome-wide methylation profiling by high-throughput sequencing of tissue (resident) versus blood circulating memory T lymphocyte populations

  This study contains RRBS data generated from 54 ex vivo samples, including CD4+ Trm (2x intestine, 2x lung, and 3x skin), CD4+CD69- tissue cells (2x bone marrow, 2x spleen, 2x intestine, 2x lung, and 3x skin), CD8+ Trm (2x bone marrow, 2x spleen, 2x intestine, 2x lung, and 3x skin), CD8+CD69- tissue cells (2x bone marrow, 2x spleen, 2x intestine, 2x lung, and 2x skin), blood CD4+ (7x) and CD8+ (8x) memory T cells.

  Study EGAS50000000085

• CIRCLE-seq of PDO

  CIRCLE-seq data of PDAC 1 patient-derived organoid (PDO) - Unmapped reads, libraries were sequenced using the Illumina NextSeq500 with the NextSeq 500/550 Mid Output Kit v2.5 (300 Cycles), generating around 10M paired end 150bp reads per sample

  Dataset EGAD50000000281

• Whole Genome Sequencing of 44 Chronic Lymphocytic Leukemia

  Whole Genome Sequencing of 44 patients with Chronic Lymphocytic Leukemia. This dataset comprises 44 .bam files aligned to the hg19 build of the human genome from sequencing reads generated on an Illumina HiSeq instrument.

  Dataset EGAD00001004384

• Rapid Idiosyncratic Mechanisms of Clinical Resistance to KRAS G12C Inhibition

  Using deep RNA and whole exome sequencing of pre- and post-treatment autopsy samples, we reveal diverse clonal populations that occurred through altered cell intrinsic, tumor microenvironment and immunologic remodeling mechanisms of resistance.

  Study phs002734

• Paired data of primary and relapse central nervous system lymphoma and testicular lymphoma

  Shallow whole genome sequencing and targeted sequencing of 33 primary - relapse samplepairs of primary central nervous system lymphoma and primary testicular lymphoma.19 Testis - contralateral testis pairs9 Testis - CNS 5 CNS - Testis

  Study EGAS00001005833

• Ribosomal Depleted Total RNA-Seq of PBMCs and Skin from Controls and Systemic Sclerosis Patients

  This study involved prospective collection of skin biopsies and peripheral blood mononuclear cell (PBMC) samples from controls with no self-reported history of autoimmune or inflammatory disease and cases with Rheumatologist-confirmed systemic sclerosis: limited cutaneous systemic sclerosis (lcSSc), diffuse cutaneous systemic sclerosis (dcSSc), very early diagnosis of systemic sclerosis (VEDOSS), and systemic sclerosis sine scleroderma (SSS). Some SSc cases were sampled at a 6 month routine follow-up visit. PBMCs were collected and lysed immediately. Skin punches were stabilized in RNAlater until extraction. All RNA-Seq libraries were created using Takara/Clontech ribosomal depletion kits, and sequenced on either a HiSeq2500 or HiSeq3000.

  Study phs002902

• 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

• Exploring_the_landscape_of_somatic_mutations_in_normal_tissue___POL___TGS_

  Somatic mutations (burdens and signatures) and clonal dynamics in individuals with germline DNA polymerase mutations.

  Study EGAS00001003754

• DNA methylation changes associated with hyperglycemia in type 1 diabetes

  This dataset includes DNA methylation profiles from 112 young with Type 1 Diabetes (T1D) at T1D diagnosis, who were longitudinally monitored for hyperglycemia over an average duration of 3 years. These datasets were generated using whole-genome bisulfite sequencing. It includes 1872 fastq files (i.e. 936 paired-end fastq files) generated through 150 bp paired-end sequencing on Illumina HiSeqX.

  Dataset EGAD50000000545

• 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

• 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 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

• ICGC PCAWG Dataset: GACA-CN_PCAWG_WGS_BWA

  ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: GACA-CN.

  Dataset EGAD00001003132

• SA501X3F direct library preparation (DLP) single-cell genomes

  Microfluidic direct library preparation (DLP) single-cell whole-genome BAM files for third-passage patient-derived primary triple-negative breast cancer xenograft SA501X3F.

  Dataset EGAD00001003149

• SA501X4F direct library preparation (DLP) single-cell genomes

  Microfluidic direct library preparation (DLP) single-cell whole-genome BAM files for fourth-passage patient-derived primary triple-negative breast cancer xenograft SA501X4F.

  Dataset EGAD00001003150

• 184-hTERT-L2 direct library preparation (DLP) single-cell genomes

  Microfluidic direct library preparation (DLP) single-cell whole-genome BAM files for near-diploid immortalized breast epithelial cell line 184-hTERT-L2.

  Dataset EGAD00001003152

• Pulldown DNA methylation study v2

  Pilot study to set up sequencing protocols for targeted pulldown methylation profiling

  Dataset EGAD00001001242

• OCCAMS_Oesophageal Cancer Organoids_1

  ***THIS DATA CAN ONLY BE USED FOR NON-COMMERCIAL CANCER RESEARCH*** Sequencing of organoid cell lines derived from oesophageal tumour sections taken from patients diagnosed with primary oesophageal cancer who underwent tumour resection surgery.

  Dataset EGAD00001001889

• Sequencing data for ICGC Oesophageal Adenocarcinoma tissue samples - ds_190916_2

  ICGC Oesophageal Adenocarcinoma tissue samples

  Dataset EGAD00001002689

• bulkRNA

  Bulk RNA-seq for cALL patient-derived PDX samples

  Dataset EGAD00001006133

• scRNA PDX

  Single cell RNA-seq for PT1-derived PDX samples

  Dataset EGAD00001006134