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• BLUEPRINT September 2016, ChIPmentation Acute Lymphocytic Leukemia for precursor B cell from bone marrow, on Genome GRCh38

  ChIPmentation data for 7 sample(s) Acute Lymphocytic Leukemia for precursor B cell from bone marrow, on Genome GRCh38. 13 run(s), 13 experiment(s), 13 alignment(s). Part of BLUEPRINT (September 2016).

  Dataset EGAD00001002928

• BLUEPRINT September 2016, ChIPmentation for memory B cell from venous blood, on Genome GRCh38

  ChIPmentation data for 2 sample(s) for memory B cell from venous blood, on Genome GRCh38. 6 run(s), 4 experiment(s), 4 alignment(s). Part of BLUEPRINT (September 2016).

  Dataset EGAD00001002923

• BLUEPRINT September 2016, ChIP-Seq for thymocyte from thymus, on Genome GRCh38

  ChIP-Seq data for 5 sample(s) for thymocyte from thymus, on Genome GRCh38. 17 run(s), 17 experiment(s), 17 alignment(s). Part of BLUEPRINT (September 2016).Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811

  Dataset EGAD00001002947

• Targeted Capture DNA Sequencing

  We performed targeted capture DNA sequencing for 29 genes in extranodal NK/T-cell lymphoma, nasal type (n=67).

  Study JGAS000548

• WTCCC2 Schizophrenia study

  A WTCCC2 project genome-wide case-control association study for schizophrenia (SP) in individuals from Ireland.

  Study EGAS00000000118

• Single-cell Full Transcriptome RNA sequencing

  Single cell full transcriptome sequencing of CD19 CAR T-cell infusion products used for standard of care treatment for relapsed/refractory large B-cell lymphoma.

  Dataset EGAD50000000201

• Targeted sequencing using SPET for Mesothelioma.

  Targeted sequencing using SPET for Mesothelioma.

  Dataset EGAD00001001916

• RNA-Seq for PTPN1 project (EGAS00001000554)

  Fastq files corresponding to RNA-Seq dataset for PTPN1 project (EGAS00001000554)

  Dataset EGAD00001001646

• DATA FILES FOR MULLIGHAN MEF2D RNASEQ STRANDED

  DATA FILES FOR MULLIGHAN MEF2D RNASEQ STRANDED

  Dataset EGAD00001002692

• DATA FILES FOR MULLIGHAN MEF2D RNASEQ UNSTRANDED

  DATA FILES FOR MULLIGHAN MEF2D RNASEQ UNSTRANDED

  Dataset EGAD00001002704

• RNASeq files for Mullighan Leventaki ALCL Project

  RNASeq files for Mullighan Leventaki ALCL Project paper titled "Integrative molecular analysis of pediatric Anaplastic large cell lymphoma reveals subtypes with distinct immune suppression signatures."

  Dataset EGAD00001005951

• Single-cell Full Transcriptome RNA sequencing

  Single cell full transcriptome sequencing of CD19 CAR T-cell infusion products used for standard of care treatment for relapsed/refractory large B-cell lymphoma.

  Dataset EGAD00001006325

• Single cell targeted RNA sequencing

  Single cell hybrid-capture targeted sequencing of CD19 CAR T-cell infusion products used for standard of care treatment for relapsed/refractory large B-cell lymphoma.

  Dataset EGAD00001006327

• Tumour sample for patient SA1058

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

  Dataset EGAD00001009673

• Tumour sample for patient SA998

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

  Dataset EGAD00001009674

• WES for Patient 1 to 8 of NIBIT-M4 clinical trial

  WES for Patient 1 to 8 of NIBIT-M4 clinical trial

  Dataset EGAD00001009701

• WGS files for paper titled "Patient-derived pediatric brain tumor organoids faithfully recapitulate primary tumors"

  WGS files for paper titled "Patient-derived pediatric brain tumor organoids faithfully recapitulate primary tumors"

  Dataset EGAD00001015800

• WXS files for paper titled "Patient-derived pediatric brain tumor organoids faithfully recapitulate primary tumors"

  WXS files for paper titled "Patient-derived pediatric brain tumor organoids faithfully recapitulate primary tumors"

  Dataset EGAD00001015801

• RNASeq files for paper titled "Patient-derived pediatric brain tumor organoids faithfully recapitulate primary tumors"

  RNASeq files for paper titled "Patient-derived pediatric brain tumor organoids faithfully recapitulate primary tumors"

  Dataset EGAD00001015802

• Raw sequencing data from chromosome conformation capture, RNA sequencing and chromatin assays in human primary monocytes

  This dataset contains raw sequencing data from eQTL Capture Hi-C, ATAC-seq and RNA-seq experiments in monocytes isolated from 34 healthy male donors, as well as from Hi-C, 4C-seq and CTCF ChIP-seq in subsets of individuals. The data are released as paired-end Illumina FASTQ files. Hi-C and Capture Hi-C used DpnII digestion and Tn5-based low-input library preparation. In Capture Hi-C, this was followed by targeted capture with custom-designed biotinylated RNA probes targeting ~1100 eQTL regions. ATAC-seq was performed on PFA-fixed cells using a digitonin-based protocol. 4C-seq and CTCF ChIP-seq were performed using standard protocols.

  Dataset EGAD50000001116

• Exome sequences of AL amyloidosis (ALA), multiple myeloma (MM) and ALA+MM hematological malignancies

  DNA was isolated from aberrant plasma cells (aPCs) and peripheral blood of 12 ALA, 10 ALA+MM and 29 MM individuals. DNA from aPCs was amplified using REPLI-g Mini Kit (Qiagen). Totally, we analyzed 51 patients, 102 samples. One batch of exome libraries (paired tumor-normal samples from 12 ALA, 10 ALA+MM and 6 MM) was prepared using SureSelect Human All Exon V5 Kit (Agilent Technologies) and sequenced on Illumina HiSeq 4000 platform, 100 cycles. Second batch (23 MM samples; IDs ARK01-ARK26) was prepared using SureSelect Human All Exon V5 + IGH, IGK, IGL, MYC (Agilent Technologies) library preparation kit and sequenced on Illumina HiSeq 2000 platform in paired-end settings, 75 cycles. The reads were mapped using BWA-MEM on human genome GRCh38 without alternate loci.

  Dataset EGAD00001006047

• Genome-wide identification of distinct miRNA-mRNA target regulation pairs in Non-Hodgkin lymphomas: a report from the ICGC MMML-Seq consortium

  We obtained miRNA profiles by miRnome sequencing from ICGC MMML-Seq patients diagnosed with Burkitt lymphoma, diffuse large B-cell lymphoma and follicular lymphoma and provide evidence of subtype-specific miRNA expression differences. We describe differentially expressed, mutated, edited and not previously annotated miRNAs. Addditionally, by performing argonaute-2 photoactivatable ribonucleoside-enhanced cross-linking and immunoprecipitation (PAR-CLIP) experiments, we obtained a set of biochemically-validated miRNA binding sites and identified miRNA-mRNA interaction pairs with a negative correlation in patient RNASeq data.

  Study EGAS00001001394

• Identifying the Genetic Basis of Variably Protease-Sensitive Prionopathy (VPSPr)

  Design: Sequencing of cases onlyMolecular technologies: Exome sequencing and custom targeted sequencing of PRNPAims: Identify modestly penetrant, high odds ratio variants conferring risk of variably protease-sensitive prionopathy (VPSPr)Population: n=67 autopsy-confirmed VPSPr cases, United States, 1997-2021Principal findings: Association to PRNP M129V replicated, no other causal variants identifiedData available: Raw sequencing data and metadata

  Study phs004012

• PBMC scRNA-seq data using 10X Genomics platform

  Matrices of counts from single-cell RNA-seq data and single-cell CITE-seq data collected from 16 patients enrolled in GO30103 trial, and the cell level annotation. Specifically, PBMCs at C1D1, C1D15 (2 weeks after treatment), C2D1 (3 weeks after treatment) and C4D1 (9 weeks after treatment) were collected and subject to 10x Genomics protocol. Associated metadata also included.

  Dataset EGAD50000000370

• Exome and RNA sequencing data from 32 ocular and extraocular sebaceous carcinomas

  Sebaceous carcinomas (SeC) are cutaneous malignancies that, in rare cases, metastasize and prove fatal. Here we report whole exome sequencing on 32 SeC, revealing distinct mutational classes that explain both cancer ontogeny and clinical course. A UV-damage signature predominated 10/32 samples, while 9 were instead defined by microsatellite instability (MSI) mutations. UV-damage SeC exhibited poorly differentiated, infiltrative histopathologycompared to MSI signature SeC (p = 0.003), features previously associated with dissemination. Strikingly, UV-damage SeC transcriptomes and anatomic distributionclosely resembling those of cutaneous squamous cell carcinomas (SCC), implicating sun-exposed keratinocytes as a cell of origin. Like SCC, this UV-damage subclass harbors a high somatic mutation burden with >50 mutations/Mb, predicting immunotherapeutic response. In contrast, ocular SeC acquire far fewer mutations without a dominant signature, but show frequent truncating mutations in the ZNF750 epidermal differentiation regulator. Our data exemplify how different mutational processes convergently drive histopathologically related but clinically distinct cancers.

  Study EGAS00001002869