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• FFPE cohort with RNA-seq data of tumor samples

  This dataset contains RNA-seq raw data in fastq format from 14 tumor samples. The samples are from primary tumors or metastasis and represent various cancer entities. The samples are formalin-fixed paraffin-embedded (FFPE) treated. For target enrichment SureSelect XT Human All Exon V6 was used. The libraries were sequenced in paired-end mode (2 x 50 nt) on a NovaSeq6000 S2 flow cell.

  Dataset EGAD00001006781

• Sequencing data for oesophageal and related samples - OACs release 5 (RNA)

  Dataset EGAD00001005383

• Sequencing data for oesophageal and related samples - BOs release 6 (RNA)

  Dataset EGAD00001005377

• Sequencing data for oesophageal and related samples - Normals release 6 (RNA)

  Dataset EGAD00001005376

• Sequencing data for oesophageal and related samples - Normals release 2 (RNA)

  Dataset EGAD00001003838

• Sequencing data for ICGC Oesophageal Adenocarcinoma tissue samples - pilot normal and pre/post-chemo

  Dataset EGAD00001000704

• RNA sequencing data of pediatric TCF3::PBX1 acute lymphoblastic leukemia (set 1)

  The dataset includes RNA sequencing FASTQ files from a diagnostic tumor sample of one TCF3::PBX1 ALL patient (ALLT-335). NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs) was used in library preparation, and Globin-Zero Gold rRNA Removal Kit (Illumina) was utilized for rRNA removal. The diagnostic tumor sample was sequenced using Illumina Novaseq 6000, and the target sequencing depth was 21 Gb.

  Dataset EGAD50000002577

• RNA sequencing data of pediatric TCF3::PBX1 acute lymphoblastic leukemia (set 2)

  The dataset includes RNA sequencing FASTQ files from a diagnostic tumor sample of one TCF3::PBX1 ALL patient (ALLT-376). NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs) was used in library preparation, and TruSeq Stranded Total RNA Library Prep (Illumina) kit was utilized for rRNA removal. The diagnostic tumor sample was sequenced using Illumina Novaseq 6000, and the target sequencing depth was 21 Gb.

  Dataset EGAD50000002578

• RNA sequencing data of pediatric BCR::ABL1 acute lymphoblastic leukemia (set 1)

  The dataset includes RNA sequencing FASTQ files from a diagnostic tumor sample of one BCR::ABL1 ALL patient (ALLT-343). NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs) was used in library preparation, and Globin-Zero Gold rRNA Removal Kit (Illumina) was utilized for rRNA removal. The diagnostic tumor sample was sequenced using Illumina Novaseq 6000, and the target sequencing depth was 21 Gb.

  Dataset EGAD50000002579

• RNA sequencing data of pediatric KMT2A-rearranged acute lymphoblastic leukemia (set 3)

  The dataset includes RNA sequencing FASTQ files from a diagnostic tumor sample of one KMT2A-r ALL patient (ALLT-375). NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs) was used in library preparation, and TruSeq Stranded Total RNA Library Prep (Illumina) kit was utilized for rRNA removal. The diagnostic tumor sample was sequenced using Illumina Novaseq 6000, and the target sequencing depth was 21 Gb.

  Dataset EGAD50000002581

• RNA sequencing data of pediatric ETV6::RUNX1 acute lymphoblastic leukemia (set 1)

  The dataset includes RNA sequencing FASTQ files from a relapse sample of one ETV6::RUNX1 ALL patient (ALLT-341). NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs) was used in library preparation, and Globin-Zero Gold rRNA Removal Kit (Illumina) was utilized for rRNA removal. The relapse sample was sequenced using Illumina Novaseq 6000, and the target sequencing depth was 21 Gb.

  Dataset EGAD50000002588

• RNA sequencing data of pediatric ETV6::RUNX1 acute lymphoblastic leukemia (set 5)

  The dataset includes RNA sequencing FASTQ files from a diagnostic tumor sample of one ETV6::RUNX1 ALL patient (ALLT-380). NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs) was used in library preparation, and TruSeq Stranded Total RNA Library Prep (Illumina) kit was utilized for rRNA removal. The diagnostic tumor sample was sequenced using Illumina Novaseq 6000, and the target sequencing depth was 21 Gb.

  Dataset EGAD50000002591

• RNA sequencing data of pediatric B-other acute lymphoblastic leukemia (set 3)

  The dataset includes RNA sequencing FASTQ files from diagnostic tumor samples of two B-other ALL patients (ALLT-369, ALLT-378). NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs) was used in library preparation, and TruSeq Stranded Total RNA Library Prep (Illumina) kit was utilized for rRNA removal. The diagnostic tumor samples were sequenced using Illumina Novaseq 6000, and the target sequencing depth was 21 Gb.

  Dataset EGAD50000002600

• 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

• V2 Colorectal panel test

  Targeted gene screen of cell line tumour samples for testing the new V2 Colorectal gene panel.

  Dataset EGAD00001003253

• oncogenic gene fusions in primary colon cancers

  This dataset represents RNA-sequencing data from 278 primary colon cancers obtained from fresh-frozen tumor sections. RNA-sequencing was performed using TruSeq library preparation and samples were sequenced on Illumina NextSeq and HiSeq. The data are available as Illumina NextSeq and HiSeq fastq files (_R1.fastq and _R2.fastq for each tumor sample, 556 files in total).

  Dataset EGAD00001003291

• 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

• Next generation sequencing data of circulating tumor DNA and matched tumor tissues

  For each subject, genomic DNA from whole blood, circulating cell free DNA and tumor tissues (whenever possible) were performed targeting next generation sequencing on Illumina Miseq or Hiseq 4000 platforms. The sequencing results of whole blood were used to distinguish germline and somatic mutations. Specimens were collected from patients with different kinds of solid tumors, but most are lung cancer patients.

  Dataset EGAD00001003176

• 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

• Exome reads

  This dataset contains WES data (.bam files) and associated phenotype information from 10 patients included in our microbiome study who went on to anti PD-1 immunotherapy for the treatment of metastatic melanoma at the University of Texas MD Anderson Cancer Center. Both tumor and matching germ line normal were sequenced on each patient using Illumina HiSeq 2500. The average coverage was 283X in tumors and 135X in germline (tumor+germline overall:209, Range: 0-1552).

  Dataset EGAD00001003797

• 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

• Anaplastic Thyroid Cancer aligned sequence data

  Sequence data in fastq format was aligned to the GRCH38 reference genome. Aligned sequence was preprocessed with GATK for Indel Realignment and Base Quality Score Recalibration. Duplicates were marked with Picard Mark Duplicates. Aligned sequence is in bam format. Details of the alignment can be found int he bam header. In total, data generated from 174 tumour samples 102 matched blood normal controls was aligned. Tumour samples were classified as Anaplastic Thyroid, Poorly-differentiated or well-differentiated cancers.

  Dataset EGAD00001004126

• Anaplastic Thyroid Cancer germline variants

  Sequence was aligned to the GRCH38 reference genome. Aligned sequence was analyzed with GATK Haplotype Caller, to generate germline variant calls across the SureSelect All Exon V5+UTR target region. Variant calls are in VCF format. In total there are samples from 173 donors. 101 donors have calls generated from both normal and tumour samples tumour samples, 94 of which have a matched normal. Details for the call can be found in the vcf headers.

  Dataset EGAD00001004127

• WES analysis of patients with USP8 wild-type corticotroph adenomas

  The overall goal of the Identification of recurrent mutations in Cushing’s disease project is to study the impact of whole-exome sequencing (WES) on the clinical care of cancer patients and oncology provider practices. The aims of Project are to implement and establish the feasibility of WES in patients with USP8 wild-type corticotroph adenomas; to develop a framework for the understanding of the molecular mechanism of the pathogenesis of corticotroph adenoma.

  Dataset EGAD00001004136

• Transcriptome sequencing of myelodysplasia

  Transcriptome sequencing was performed on 214 patients with myelodysplasia in this study. RNA was obtained from bone marrow CD34+ cells (n=100) and/or bone marrow mononuclear cells (n=165). Transcriptome sequencing was performed for both cell fractions in 51 patients. A total of 211 patients were genotyped by targeted deep sequencing. We also studied bone marrow CD34+ cells and bone marrow mononuclear cells obtained from three healthy adults each.

  Dataset EGAD00001003891

• Circular RNA characterization in functionally distinct brain regions

  RNA extracted from middle temporal gyrus (MG) brain region of healthy elderly controls. Three pairs of samples were generated, each pair consisting of one sample that was enriched for circular RNAs using RNase R, and a second sample that was not enriched (total N=6). Remaining samples in the study from other functionally distinct brain regions are currently under process and will be released soon.

  Dataset EGAD00001004211

• 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

• Clonal cultures of T memory cells

  Sequence data (bam files) of two RRBS samples for paper "A comprehensive analysis of 195 DNA methylomes reveals shared and cell specific features of partially methylated domains". Short Description: CD4+ T memory cells (CD3+ CD4+ CD45RA- CD45RO+ CD25-) from donors were sorted by flow-cytometry either as a bulk culture ('ex vivo' sample) or in a single-cell format into 96 well-plates ('clone' sample) in the presence of a TCR stimulus.

  Dataset EGAD00001004303

• Resolving the Full Spectrum of Human Genome Variation using Linked-Reads

  This dataset contains Linked-Read Whole Exome Sequencing (lrWES) from individuals with known disease-causing variants. The dataset comprises of 30 samples from 10 donors, where multiple samples from the same donor reflect experimental differences assaying the effect of input DNA length on coverage and phasing. Raw data (i.e. BAM files) and variant analysis (i.e. VCF files) for each sample are included in this dataset.

  Dataset EGAD00001004319

• 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

• 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

• NIHR BioResource Rare Diseases WGS project - Stem cell and Myeloid Disorders (SMD) Rare Disease domain

  Short read whole genome sequencing (WGS) CRAM files for the NIHR BioResource Rare Diseases WGS project – Participants from the Stem cell and Myeloid Disorders (SMD) Rare Disease domain

  Dataset EGAD00001004524

• NIHR BioResource Rare Diseases WGS project - Pulmonary Arterial Hypertension (PAH) Rare Disease domain

  Short read whole genome sequencing (WGS) CRAM files for the NIHR BioResource Rare Diseases WGS project – Participants from the Pulmonary Arterial Hypertension (PAH) Rare Disease domain

  Dataset EGAD00001004525

• 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

• EORTC study on the evolution of driver mutations and MGMT promotor methylation in glioblastomas treated with standard of care: Correlation with survival and impact on trial design

  Precision medicine trials in glioblastoma should be conducted at tumor recurrence. However, second surgery for recurrent GBMs is not routinely performed and therefore molecular data is predominantly derived from primary samples. This study aims to establish the frequency of driver changes at tumor recurrence.

  Dataset EGAD00001004593

• 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

• Whole genome bisulfite sequencing data of human monocyte sample 43_Hm01_BIMo_Ct from healthy male donor.

  Human monocytes from a healthy male blood donor were obtained after written informed consent and anonymised. Library preparation was performed essentially as described in the “Whole‐genome Bisulfite Sequencing for Methylation Analysis (WGBS)” protocol as released by Illumina. The library was sequenced on an Illumina HiSeq2500 using 101 bp paired-end sequencing. Read mapping was done with BWA.

  Dataset EGAD00001001390

• Pulldown DNA methylation study v2

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

  Dataset EGAD00001001242

• 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

• 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

• Cancer initiation organoids BAM files

  This dataset contains whole-genome sequencing data files from colon organoid cultures, which were mutated using CRISPR-Cas9 for specific genes (APC, KRAS, TP53 and SMAD4) to generate in vitro transformed cancer cells. After introducing each mutation, the resulting cultures were subjected to whole-genome sequencing. In addition, some cultures were xenotransplanted in recipient mice. The resulting primary tumors and corresponding metastases were subjected to whole-genome sequencing.

  Dataset EGAD00001002719

• Transcriptome profiling of prostate tissue samples from early onset prostate cancer patients and normal controls by RNA-seq

  The dataset contains RNA-seq data of 96 EOPC patients and 9 controls. For some patients multiple tissue samples were sequenced ("multi-area" samples). The RNA extraction and sequencing protocol was earlier described in Weischenfeldt et al, Cancer Cell, 2013.

  Dataset EGAD00001004791

• RNA-seq of human glioblastoma and matched gliomasphere cell lines (BLN panel)

  This dataset contains all RNA-seq runs for the BLN panel of cell lines and matched parental tumors. Tumor/cell line pairs have been authenticated using SNP profiles and all pairs were confirmed. Please note: The dataset also contains raw data from an early primary culture (BLN-1) where no stable cell line could be generated. Please also note different reference genomes.

  Dataset EGAD00001002893

• RNA sequencing of NK cells in human lung

  The dataset contains RNAseq data from 5 subsets of NK cells isolated from human lung: 1) CD69+CD49a+CD103+CD16-CD56bright NK cells 2) CD69+CD49a+CD103-CD16-CD56bright NK cells 3) CD69+CD49a-CD103-CD16-CD56bright NK cells 4) CD69-CD49a-CD103-CD16-CD56bright NK cells 5) CD56dimCD16+NKG2A+CD57- NK cells The dataset contains paired data for the subsets from 2 donors with 2 biological replicates/donor and subset.

  Dataset EGAD00001004850