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• WXS Normal Samples Javelin head and neck 100

  We performed Whole Exome (WXS) and RNASeq sequencing on samples obtained from the phase 3 randomized, double-blinded, placebo-controlled study in patients with locally advanced squamous cell carcinoma of the head and neck JAVELIN Head and Neck 100 (NCT02952586). There are 471 WXS Tumor samples and 346 RNASeq tumor samples. All tumor samples have matching normal samples.

  Dataset EGAD00001011321

• Exome sequencing data from two small cell prostate cancer patients

  Exome sequencing data from two small cell prostate cancer patients - 4 cancer samples (FFPE) from Patient 1 collected at 3 different time points and 2 cancer samples (FFPE) from Patient 2 collected at 1 time point. Exonic DNA was enriched using the TruSeq Exome Kit (Illumina) and sequenced on the Illumina NextSeq 500 as 75bp paired end reads (total read length 150bp).

  Dataset EGAD00001011149

• WES data of central nervous system neoplasm patients

  Dataset containing 2068 WES tumor and control samples of central nervous system neoplasm patients. The data was sequenced on a Illumina NextSeq 500 using a NPHD2015A kit. The sequencing was always paired.

  Dataset EGAD00001009855

• Failure of Differentiation of the Rhombic Lip Constitutes Medulloblastoma

  We used single-cell transcriptomics to study cells from the developing human cerebellum, and show that different molecular subgroups of medulloblastoma resemble distinct glutamatergic progenitors.

  Dataset EGAD00001008381

• Acute myeloid leukemia whole exome sequencing (Diagnosis, Complete Remission and Relapse)

  To gain insight into the clonal heterogeneity of diagnosis (Dx) and relapse (Re) pairs, we employed whole exome sequencing to longitudinally profile two t(8;21) (AML1-ETO = RUNX1-RUNX1T1), and four FLT3-ITD AML cases. All the samples are bone marrow aspirates.

  Dataset EGAD00001008375

• RNA sequencing of Human Organoid Lines

  The study will use RNA sequencing to aid in benchmarking different culture conditions in a set of genetically annotated human organoid lines. The data will be used to assess whether there are any clonal differences introduced when culturing these lines in different conditions.

  Dataset EGAD00001007971

• Bulk RNAseq data of scrambled and siRNA-mediated knock-down of the minor spliceosome snRNA U6atac

  Bulk RNAseq data of scrambled and siRNA-mediated knock-down of the minor spliceosome snRNA U6atac in androgen-sensitive LNCaP cells (L), androgen-insensitive C4-2 (C) and 22Rv1 (R) cells and in patient derived neuroendocrine organoids PM154 (P).

  Dataset EGAD00001008034

• Paired-WGS-two-families-with-GBA-variants-and-Parkinsons-disease

  We performed whole- genome sequencing, rare variant filtering, segregation analysis and functional validation of PD cosegregating rare genetic variation in two families (6 samples) segregating PD associated GBA variants c.115+1G>A (ClinVar ID: 93445, ) and p.L444P (ClinVar ID: 4288) respectively. The paired WGS sequencing was run on HiSeq X Ten and the library preparation kit was Illumina TruSeq DNA nano.

  Dataset EGAD00001006561

• A spatiotemporal organ-wide gene expression and cell atlas of the developing human heart

  Dataset includes 2 scRNA-seq samples from a 6.5-7 post-conception weeks human embryonic heart and 19 samples from 4.5-9 post-conception weeks human embryonic hearts analyzed with the Spatial Transcriptomics method. H&E stains can be sent if requested.

  Dataset EGAD00001005468

• RNA Sequencing of Colorectal Liver Metastases

  Reverse-stranded paired-end 75 base-pair RNA sequencing libraries of 93 metastatic FFPE samples were constructed using Illumina Total RNA Stranded Kits. Ribosomal RNAs (rRNAs) were depleted by using the Ribo-Zero rRNA Removal Kit (Illumina). Libraries were sequenced on a HiSEQ2500 machine. Five samples were re-sequenced using paired-end 50 base-pair libraries due to the smaller insert sizes.

  Dataset EGAD00001004111

• Whole-exome sequencing of P2RY8-CRLF2-positive ALL on Illumina HiSeq 2000, 100 bp paired-end

  Genomic DNA from leukemic and remission bone marrow mononuclear cells was isolated with the QIAamp DNA Blood Extraction Kit (Qiagen, Venlo, The Netherlands). Libraries were prepared using Nextera Rapid Capture Exome Kit (Illumina, San Diego, USA). Paired-end sequencing of 100 bp reads was performed on a HiSeq 2000 (Illumina) to obtain at least a 50 x coverage.

  Dataset EGAD00001002666

• A single-cell multi-omic atlas of nodal B-cell non-Hodgkin lymphomas

  Nodal B-cell non-Hodgkin lymphomas (B-NHL) are a clinically diverse set of cancers thought to originate from distinct stages of B-cell maturation. To characterize intratumor heterogeneity across B-NHL entities, we performed CITE-Seq (cellular indexing of transcriptomes and epitopes) on 51 lymph node samples including mantle cell lymphoma (MCL, n = 8), follicular lymphoma (FL, n = 12), germinal center (GCB, n = 5) or activated B-cell (non-GCB/ABC, n = 7) diffuse large B-cell lymphoma (DLBCL) and marginal zone lymphoma (MZL, n = 11) tumors, in addition to non-malignant reactive lymph nodes (rLN, n = 8). We also performed 5 prime scRNA-seq with immune receptor profiling for 11 of these samples (2 rLN, 2 MCL, 3 FL, 2 DLBCL, and 2 MZL).

  Study EGAS50000000342

• A108846B

  Whole genome sequencing for single cells for library A108846B 1636 cells; filetype=bam

  Dataset EGAD00001007092

• Data Access Commitee of the Kok group, NKI

  Dac EGAC00001003025

• Department of Pediatrics, The University of Tokyo Data Access Committee

  Dac EGAC00001000207

• DAC of the chronic lymphocytic leukemia epigenome and transcriptome profiling project

  Dac EGAC00001000486

• DAC to control data accession to the Myeloproliferative Neoplasm transcriptome study

  Dac EGAC00001001134

• Total RNAseq in the sporadic ALS and healthy control motor cortex

  Dac EGAC00001001515

• The University of Hong Kong Intestinal Metaplasia Organoids Study

  Dac EGAC00001003502

• Elucidating the molecular landscape of KRAS/BRAF mutant colorectal cancers

  Study EGAS00001007459

• The admixture histories of Cabo Verde

  Study EGAS00001006348

• Study of the microenvironment of angioimmunoblastic T-cell lymphoma

  Study EGAS00001006401

• Enhancer-gene rewiring in the pathogenesis of Quebec Platelet Disorder

  Study EGAS00001004315

• Genetic Effects on the Skin Methylome in Healthy Older Twins

  Study EGAS00001007816

• CeD_Italy

  Association results from the Italian cohort

  Dataset EGAD00010001771

• CeD_Ireland

  Association results from the Irish cohort

  Dataset EGAD00010001769

• CeD_Netherlands

  Association results from the Dutch cohort

  Dataset EGAD00010001764

• Department of Pediatrics, The University of Tokyo, PPB Data Access Committee

  Dac EGAC00001000163

• Longitudinal DNA methylation in the Lothian Birth Cohorts of 1921 and 1936

  Dac EGAC00001000218

• The Ingham Institute Gastro-Intestinal Viral Oncology Group Genome Data Access Committee

  Dac EGAC00001000367

• DAC of the BRITROC project

  Dac EGAC00001000388

• The Danish Reference Genome - GenomeDenmark data access committee

  Dac EGAC00001000562

• MeDIP-seq data in the Peri/postnatal Epigenetics Twins Study (PETS)

  Dac EGAC00001000596

• Data Access Commitee of The First Affiliated Hospital of Nanjing Medical University

  Dac EGAC00001001209

• The Lothian Birth Cohorts Data Access Committee

  Dac EGAC00001001376

• The Egyptian Collaborative Cardiac Genomics Project Data Access Committee (ECCO-GEN DAC)

  Dac EGAC00001001594

• The Egyptian Collaborative Cardiac Genomics Project Data Access Committee (ECCO-GEN DAC)

  Dac EGAC00001001680

• Variation and transmission of the human gut microbiota across generations - 16S data

  Dac EGAC00001002344

• Variation and transmission of the human gut microbiota across generations - shotgun data

  Dac EGAC00001002355

• Data Access Committee of the Department of Molecular Neurology, UKEr

  Dac EGAC00001002695

• DAC - U1085 Team Physiology and Physiopathology of the urogenital tract (INSERM / IRSET)

  Dac EGAC00001002830

• ATAC-Seq and CTCF ChIP-Seq on the OCIAML-2 cell line

  Study EGAS00001004741

• TULIPs decorate the three-dimensional genome of PFA ependymoma

  Study EGAS00001005476

• The effects of inhaled corticosteroids on healthy airways

  Study EGAS00001007538

• A critical spotlight on the paradigms of FFPE-DNA sequencing

  Study EGAS00001005757

• DNA methylation profiles of samples included in the EORTC 26091 TAVAREC trial

  Study EGAS00001006015

• Measuring the Efficiency of Purging by Nonrandom Mating in Human Populations

  Study EGAS00001007831

• CeD_meta_analysis

  Results of the celiac diease meta-analysis

  Dataset EGAD00010001770

• CeD_Argentina_1

  Association results from the Agentinian cohort one

  Dataset EGAD00010001768

• EGAD00000000060

  Samples from the UK Glomerulonephritis DNA bank

  Dataset EGAD00000000060

• Target bisulfite sequencing of uterine cervical cancer

  We performed targeted bisulfite sequencing of the HLA-A promoter region in cervical tissue samples to investigate DNA methylation patterns that regulate immune recognition and antigen presentation, which may influence viral immune surveillance and malignant transformation in cervical pathology.

  Study JGAS000825

• Analysis of lymphocytes specific gene expression pattern by RNA-Seq in patients with IgG4-related disease: Comparison between submandibular glands and peripheral blood

  We compared the gene expression of PanT and CD19+B cells by RNA-Seq between SMGs versus PBMCs in IgG4-RD, or IgG4-RD versus pSS versus HCs in PBMCs.

  Study JGAS000630

• Prediction of response to preoperative chemoradiotherapy in rectal cancer based on whole-exome sequencing and transcriptomic analysis

  Accumulating evidence suggests that radiotherapeutic success has an immune-associated component. We aimed to investigate the immunogenomic profiles associated with response to preoperative chemoradiotherapy (CRT) in patients with locally advanced rectal cancer.

  Study JGAS000158

• Whole genome sequencing, DNA methylation, and gene expression data from gastrointestinal stromal tumor 30 patients

  We performed WGS along with genome-wide DNA methylation and gene expression analyses in 30 GIST cases to determine the genomic and epigenomic differences between KIT exon 11 557���558 deletions and other KIT exon 11 mutations.

  Study JGAS000604

• Whole exome sequence and transcliptomic analysis of tumor tissues with hepatocellular carcinoma and metastatic liver cancer

  We used our pipeline to select neoepitopes with high immunogenicity from the tumor tissues of 46 patients with hepatocellular carcinoma or metastasis of colorectal carcinoma by whole exome sequence and transcriptomic analysis with tumor tissue.

  Study JGAS000507

• Whole Genome Methylation in CLL

  We have extensively characterized the DNA methylome of chronic lymphocytic leukemia (CLL) with mutated and unmutated IGHV as well as several mature B cell subpopulations using whole-genome bisulfite sequencing and high-density microarrays.

  Study EGAS00001000272

• Genetic landscape of pediatric ependymoma

  We performed whole-genome sequencing of 42 paired tumor/normal EPD genomes and analyzed somatically acquired single nucleotide variations (SNVs), insertion/deletions, structural variations and copy number variations in the cancer genomes

  Study EGAS00001000254

• Clinical Utility of Breast cancer Research by Inocras, Catholic university hospital and Samsung medical center

  Breast cancer remains a major global challenge. To comprehensively characterize its genomic landscape and clinical significance, we analyzed whole genome sequences from 1,364 clinically annotated breast cancers, integrating transcriptome data from most of the tumors.

  Study EGAS50000001062

• Isoform-level profiling of m6A modifications in human brain

  Oxford Nanopore direct RNA sequencing (DRS) can quantify isoform expression, modifications and polyA tail lengths, enabling simultaneous investigation of the transcriptome and epitranscriptome. We applied DRS to three post-mortem human brain regions: prefrontal cortex, caudate nucleus and cerebellum.

  Study EGAS00001007742

• Clinical Utility of Breast cancer Research by Inocras, Catholic university hospital and Samsung medical center

  Breast cancer remains a major global challenge. To comprehensively characterize its genomic landscape and clinical significance, we analyzed whole genome sequences from 1,364 clinically annotated breast cancers, integrating transcriptome data from most of the tumors.

  Study EGAS50000001377

• HER2_positive_Breast_Cancer_

  We propose to definitively characterise the somatic genetics of HER2+ve breast cancer through generation of comprehensive catalogues of somatic mutations in a number of cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.

  Study EGAS00001000042

• WES data from primary CRCs tissues in ctDNA positive patients

  Whole exome data from primary colorectal cancer tissue samples were analysed in patients where mutations where found in circulating tumour DNA. DNA was extracted from FFPE blocks and exome libraries were prepared using the KAPA HyperPlus Kit (Roche diagnostics)

  Study EGAS50000000650

• Spectrum and significance of MYC and BCL2 mutations in DLBCL

  We analyzed the spectrum and clinical significance of MYC and BCL2 mutations in 347 DLBCL cases from population-based cohort of BC, Canada. Mutational status of MYC and BCL2 coding exons were sequenced using TSCA assay.

  Study EGAS00001002206

• TBA

  Analysis of mutational signatures arising in vivo in humans. iPS cells from control patients and100 patients carrying known mutations in DNA repair/editing genes will be generated, andsequenced.Blood from the patients will also be used to generate reference 'germline' sequence data.

  Study EGAS00001000802

• Balanced_Brain_Tumour_Whole_Genome_Sequencing

  We propose to definitively characterise the somatic genetics of a number of pediatric malignant tumours including ependymoma, high grade glioma and central nervous system primitive neurectodermal tumours through generation of comprehensive catalogues of somatic mutations by high coverage genome sequencing.

  Study EGAS00001000360

• TBA

  Analysis of mutational signatures arising in vivo in humans. iPS cells from control patients and100 patients carrying known mutations in DNA repair/editing genes will be generated, andsequenced.Blood from the patients will also be used to generate reference 'germline' sequence data.

  Study EGAS00001000803

• Whole genome amplification and whole genome sequencing of human single cells

  Human single fibroblasts and T-lymphocytes were amplified using multiple annealing and looping-based amplification and multiple displacement amplification. Amplified products were next subjected to whole genome sequencing with the goal of performing a genetic variant analysis.

  Study EGAS00001003108

• Genetic_Overlap_between_Metabolic_and_Psychiatric_disease

  The Genetic Overlap between Metabolic and Psychiatric Diseases (GOMAP) study comprises samples from four patient groups: 964 schizophrenia samples, 921 type 2 diabetes patients, 582 patients with comorbid schizophrenia and type 2 diabetes and 280 samples with another psychiatric diagnosis.

  Study EGAS00001002723

• Triple_Negative_Breast_Cancer_sequencing

  We propose to definitively characterise the somatic genetics of triple-ve breast cancer through generation of comprehensive catalogues of somatic mutations in a number of cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.

  Study EGAS00001000161

• Genetic landscape of pediatric Rhabdomyosarcoma

  We performed whole-genome sequencing of 13 paired tumor/normal Rhabdomyosarcoma genomes and analyzed somatically acquired single nucleotide variations SNVs, insertion/deletions, structural variations and copy number variations in the cancer genomes

  Study EGAS00001000256

• Genetic landscape of pediatric Osteosarcoma

  We performed whole-genome sequencing of 37 paired tumor/normal OS genomes and analyzed somatically acquired single nucleotide variations (SNVs), insertion/deletions, structural variations and copy number variations in the cancer genomes

  Study EGAS00001000263

• Coloured individuals from South Africa

  Genome-wide genotype array data (H3Africa_2017_20021485_A2 and H3Africa_2019_20037295_B1 arrays) of 152 individuals from different locations in South Africa and self-identified as Coloured. From the sites of Graaff-Reinet, Genadendal, Greyton, Nieu-Bethesda, Kranshoek, Prince Albert and Oudtshoorn.

  Study EGAS50000000352

• Whole genome sequencing of pediatric BCR-ABL1 positive acute lymphoblastic leukemia

  We performed whole-genome sequencing of 18 paired tumor/normal BCR-ABL1+ leukemia genomes and analyzed single nucleotide variations (SNVs), insertion/deletions, structural variations and copy number variations in the tumor and normal genomes

  Study EGAS00001000253

• MET amplification in gastric cancer

  Targeting MET in gastric and gastroesophageal junction adenocarcinoma (GC) with monoclonal antibodies or tyrosine kinase inhibitors has had limited success. We hypothesize that other prognostic and response determining genetic alterations explain the poor outcome and lack of response to MET-targeted therapies.

  Study EGAS50000000744

• TBA

  Analysis of mutational signatures arising in vivo in humans. iPS cells from control patients and100 patients carrying known mutations in DNA repair/editing genes will be generated, andsequenced.Blood from the patients will also be used to generate reference 'germline' sequence data.

  Study EGAS00001000801

• Myeloma WGS

  Most patients with multiple myeloma (MM) die from progressive disease after relapse. To advance our understanding of MM evolution mechanisms, we performed whole-genome sequencing of 80 tumour-normal newly diagnosed pairs and 24 matched relapse tumours from the Myeloma XI trial.

  Study EGAS00001004000

• SJCRH Patient-derived orthotopic xenografts of pediatric brain tumors

  Primary patient pediatric brain tumors from patients treated at SJCRH were implanted and amplified only in the brain of immunocompromised mice without tissue culture steps and referred as patient-derived orthotopic xenografts (Smith et al, Acta Neuropathologica, 2020).

  Study EGAS00001005533

• Targeted sequencing of brain AVM tissues

  We previously identified somatic activating KRAS mutations in a majority of human arteriovenous malformations (AVMs), using whole exome sequencing. We have now performed targeted sequencing on AVMS, investigating genes in the RAS-MAPK pathway, angiogenesis and brain vascular disorders among others.

  Study EGAS00001006729

• Study of Korean Parkinson's disease

  Single nucleotide variants (SNVs) associated with Parkinson’s disease (PD) have been investigated mainly through genome-wide association studies. Here, we conducted whole genome sequencing of 410 PD patients and 200 healthy individuals of the Korean population and identified disease-related SNVs.

  Study EGAS00001006811

• DNA sequencing of sgRNAs in CRISPR-Cas9 screening and RNA sequencing of SF3B4-overexpressing liver organoids

  The dataset contains 18 samples. It includs 12 paired whole genome sequencing, and 2 matched short read and long read RNA sequencing of liver organoids, 2 paired RIP RNA sequencing samples. All the experiments were performed on Illumina platform with raw reads stored in fastq format or bam format.

  Dataset EGAD50000001625

• Smart-seq2 analysis of 11 ETMR patient samples (4,031 high-quality single cells/nuclei).

  We analyzed 11 ETMR patient samples using single-cell transcriptomics (6 from fresh and 5 from frozen material). Samples were profilied by paired-end scRNA-sequencing using the Smart-Seq2 protocol on a NextSeq 500 sequencer (Illumina). The dataset contains 8,062 fastq files of 4,031 high-quality single cells/nuclei. Raw fastq files of high-quality cells are shared.

  Dataset EGAD50000001379

• Enzymatic methylation sequencing of cell-free pediatric brain tumor DNA from cerebrospinal fluid

  Enzymatic methylation sequencing data generated from cell-free tumor DNA extracted from cerebrospinal fluid (CSF). CSF was gathered from pediatric brain tumor patients of varying diagnoses treated at Connecticut Children's Medical Center, or from the Children's Brain Tumor Network. After DNA extraction, libraries were prepped using the Enzymatic Methyl-seq V2 kit (New England Biolabs).

  Dataset EGAD50000001268

• APS-1 TCR Sequencing

  Single cell TCR sequencing of expanded regulatory T cells (Tregs) in 9 APS-1 patients and 9 ange and gender matched controls. T-cell receptor (TCR) libraries were generated using the Single Cell Human TCR Amplification Kit and the Library Construction Kit from 10x genomics.

  Dataset EGAD50000000261

• Epigenome-wide association study of cocaine use disorder in postmortem human brain tissue

  Analysis of cocaine use disorder (CUD) associated epigenome-wide DNA methylation (DNAm) alterations in human postmortem brain tissue of Brodmann Area 9. Tissue samples from N=21 CUD cases and N=21 individuals without CUD originating from the Douglas Bell Canada Brain Bank (DBCBB) were included. Epigenome-wide DNAm was investigated using the Illumina Infinium MethylationEPIC array.

  Dataset EGAD00010002396

• Prospective cohort patients with Multiple sclerosis and controls

  The sys4MS cohort comprises 350 patients with Multiple Sclerosis (MS) and 9 controls, with 2 years of follow-up. Baseline data includes demographics, clinical scales, disease duration and subtype and use of disease-modifying drugs, brain MRI (volumetry and lesion load), retinal thickness by OCT, genomics (GWAS), cytomics, and phosphoproteomics. Data at the end of follow-up includes clinical scales, brain MRI and OCT.

  Dataset EGAD00010002505

• HIPO016 - glioblastoma tumour methylation microarray profiling

  Methylation microarray profiling (Illumina Human Methylation 450k and EPIC platforms) of 60 adult glioblastomas. Tumours were subtyped using the approach from Sturm et al. (https://doi.org/10.1016/j.ccr.2012.08.024): 12 IDH, 18 MES, 12 RTK I, 18 RTK II. DNA was prepared, assayed on the microarrays, and raw data computationally processed as described in Capper et al., "DNA methylation-based classification of central nervous system tumours": https://www.nature.com/articles/nature26000

  Dataset EGAD00010001797

• TRACERx NSCLC - Multiregion RNA sequencing data from the 421 cohort

  RNAseq data from the TRACERx 421 cohort

  Dataset EGAD00001009862

• GELATO clinical trial whole exome sequencing data (primary tumors and local recurrences)

  Paired-end whole exome sequencing of 10 lobular breast cancer primary tumors, 3 local recurrences and matched normal samples obtained from 10 unique patients from the GELATO clinical trial. The included raw sequencing data in fastq format was generated using Illumina NovaSeq 6000 from archived FFPE material (tumor data) and fresh frozen material (matched normal data).

  Dataset EGAD00001009836

• Paired ONT and downsampled Illumina cfDNA dataset

  The dataset contains 12 lung cancer plasma cfDNA samples, 8 bladder cancer and 2 healthy control urine cfDNA samples collected in EDTA collection tubes. Shallow WGS was performed using both Oxford Nanopore Technologies' MinION platform with an R9.4.1 flow cell and the SQK-PBK004 kit (22 files) and Illumina Novaseq platform with an S4 flow cell in PE150bp configuration (2x22 files).

  Dataset EGAD00001009392

• Acute myeloid leukemia single cell RNA-seq (Diagnosis and Relapse)

  To gain insight into the clonal heterogeneity of diagnosis (Dx) and relapse (Re) pairs, we employed single-cell RNA-seq (SORT-seq) to longitudinally profile two t(8;21) (AML1-ETO = RUNX1-RUNX1T1), and four FLT3-ITD AML cases. All the samples are Bone marrow aspirates.

  Dataset EGAD00001008373

• CM214 - Biomarker Analysis From the Phase 3 CheckMate 214 Trial of Nivolumab Plus Ipilimumab (N+I) or Sunitinib (S) in Advanced Renal Cell Carcinoma (aRCC)

  CM214 - Biomarker Analysis From the Phase 3 CheckMate 214 Trial of Nivolumab Plus Ipilimumab (N+I) or Sunitinib (S) in Advanced Renal Cell Carcinoma (aRCC)

  Dataset EGAD00001007938

• The natural history of clonal haematopoiesis: phase 6 targeted

  Deep targeted sequencing of 56 genes associated with clonal haematopoiesis and haematological malignancy in peripheral blood-derived DNA from 11 older adults, each previously sampled 2-5 times over the preceding ~13 years.

  Dataset EGAD00001007683

• Whole genome bisulfite sequencing on 10 multiple myeloma cases

  Whole genome bisulfite sequencing on 10 multiple myeloma cases. Data quality control and adaptor-trimmed were performed with the Trimomatic tool. Paired-reads were mapped to the hg19 human reference with methylCtools aligner.

  Dataset EGAD00001007821

• Prognostic and immunomodulatory consequences of ERV expression in ovarian cancer

  The dataset contains transcriptional data obtained using total RNA sequencing on a Illumina machin. 59 samples are from the Hammersmith Hospital (HH) cohort of human primary ovarian tumours and 20 samples are from ovarian cancer cell lines Kuramochi (3 replicates) and Ovsaho (2 replicates) treated with 1 uM DNMTi guadecitabine or vehicle, at an early (day 5) or late (day 8) timepoint.

  Dataset EGAD00001006589

• Single-cell RNA sequencing of cytokine-induced T cell responses

  Cytokines affect T cell responses by polarising them to different phenotypes. We isolated T cells from healthy platelet donors and cultured them in resting and stimulated condition, as well as in the presence of Th2, iTreg and Th17 polarizing cocktail. To characterize the efficacy of cytokine induced porization and subpopulation specific response, we profiled single cell transcriptome five days following polarization using 10x platform (3' v2).

  Dataset EGAD00001005290

• RNA sequencing of cytokine-induced T cell responses

  Cytokines affect T cell responses by polarising them to different phenotypes. We isolated T cells from healthy platelet donors and cultured them in resting and stimulated conditions, as well as in the presence of Th1, Th2, Th17 and iTreg cocktail. In addition, T cells were stimulated in the presence of IL-10, IL-21, IL-27, IFNb and TNFa. We performed bulk RNA sequencing to assess impact of different disease-relevant cytokines upon T cell response.

  Dataset EGAD00001005291

• Extreme intratumor heterogeneity and driver evolution in mismatch repair deficient gastro-esophageal cancer

  The dataset includes multi-region exome sequencing (MSeq) of four resected treatment naïve mismatch repair deficient gastro-esophageal cancers. Paired-end sequencing was performed on the Illumina HiSeq 2500 or NovaSeq 6000 with a target depth of 200X. Seven primary tumor regions along with tumor-adjacent non malignant tissue were subjected to MSeq. An additional two lymph node metastases were also included from each of two cases.

  Dataset EGAD00001004594

• RNA-seq of hepatocellular carcinoma xenografts established from needle biopsies

  RNA-sequencing of human hepatocellular carcinoma biopsies (n=14), 44 HCC xenografts derived from 11 HCC biopsies and 3 lymphoma xenografts derived from 3 HCC biopsies. RNA-sequencing was performed using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (lllumina). SR126 sequencing was performed on an Illumina HiSeq 2500 using v4 SBS chemistry according to the manufacturer’s guidelines.

  Dataset EGAD00001004541

• Congenital mesoblastic nephroma and infantile fibrosarcoma

  The genetic basis of many rare childhood cancers remains unknown. These include a spectrum of infant soft tissue tumors without canonical gene fusions, encompassing congenital mesoblastic nephroma (CMN) of the kidney and infantile fibrosarcoma (IFS). Here, we integrated whole genome and transcriptome sequencing and identified diagnostic markers and novel therapeutic strategies.

  Dataset EGAD00001003885

• Whole genome sequencing of 25 prostate normal and tumor pairs aligned with the CGP BWA-mem workflow.

  Whole genome sequencing data of 25 prostate tumor and corresponding normal samples, aligned with the CGP BWA-mem workflow.

  Dataset EGAD00001003835