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in 95.00 milliseconds.

• EuCanImage_DEMO_UC1

  This dataset contains the standardized clinical information related to the Use case 1 - Liver Cancer (HCC) from EuCanImage. The Data is Synthetic.

  Dataset EGAD50000002083

• Genetic Susceptibility and Biomarkers of Platinum-Related Toxicities

  The Platinum Study is an R01-funded, multicenter study of testicular cancer survivors that characterizes both long-term cisplatin-induced peripheral neuropathy (CisIPN) and cisplatin-associated ototoxicity, i.e., permanent, bilateral hearing loss. We collected data abstracted from medical records (e.g., cumulative cisplatin dose), conducted audiometric examinations, and administered self-report questionnaires, which included CisIPN symptoms.

  Study phs001621

• Washington University Coronary Artery Disease Study

  The genetic basis of coronary artery disease in individuals of non-European ancestry is largely unknown. The Washington University Coronary Artery Disease Study (WUCADS) recruited participants of non-European ancestry with and without coronary artery disease to address this question. Whole genome sequencing in WUCADS was performed at the McDonnell Genome Institute at Washington University.

  Study phs001227

• Loss of RREB1 in pancreatic beta cells reduces cellular insulin content and affects endocrine cell gene expression

  Genome-wide studies have uncovered multiple independent signals at the RREB1 locus associated with altered type 2 diabetes (T2D) risk and related glycemic traits. However, little is known about the function of the zinc finger transcription factor RREB1 in glucose homeostasis or how changes in its expression and/or function influence diabetes risk. We studied its function using three transcriptomic strategies, profiling gene expression when RREB1 is knocked out or knocked down in the Endo-betaH1 cell line, in addition to the in vitro differentiation in hiPSCs.

  Dataset EGAD00001009740

• Multi-modal single-cell analysis of salivary glands from patients with Sjogren's syndrome

  Sjogren's syndrome (SS) is an autoimmune disease that causes salivary gland dysfunction due to immune-mediated destruction. In this study, we apply multi-modal single-cell technologies - single-cell RNA sequencing and T-cell receptor sequencing - to salivary gland lesions, aiming to uncover transcriptional signatures and TCR sequence linked to autoantibody profiles.

  Study JGAS000808

• The_evolution_of_CML

  This project aims to investigate the timing of acquistion of key driver events in CML such as the canonical BCR/ABL gene fusion and their clonal trajectories in order determine selection advantage of such clones. Colonies derived from single haematopoietic progenitors will be sequenced as clonal units. This is in line with other work in the Nangalia lab and CASM.

  Study EGAS00001005095

• Whole exome sequencing from early stage non-small cell lung cancer patients at MDACC

  The purpose of the study is to evaluate the mutational landscape and tumor mutational burden in tumor from patients with early stage non-small cell lung cancer. Mutational landscape was compared to the T cell repertoire to determine the relationship between somatic mutations and T cell response in early-stage NSCLC.

  Study EGAS00001004026

• Genomic Data from Patients with Advanced Rare Cancers Treated with Pembrolizumab

  Rare cancers lack effective evidence-based treatments despite contributing substantially to cancer-related mortality. The goal of this study is to identify molecular biomarkers associated with response to pembrolizumab in patients with advanced rare cancers.This dataset includes genomic profiling generated from patients enrolled in an investigator-initiated phase II basket trial of pembrolizumab.

  Study EGAS50000001508

• Transcriptomic Data from Patients with Advanced Rare Cancers Treated with Pembrolizumab

  Rare cancers lack effective evidence-based treatments despite contributing substantially to cancer-related mortality. The goal of this study is to identify molecular biomarkers associated with response to pembrolizumab in patients with advanced rare cancers.This dataset includes transcriptomic profiling generated from patients enrolled in an investigator-initiated phase II basket trial of pembrolizumab.

  Study EGAS50000001509

• Abnormal_foetal_development_exome_trios

  This project is to explore the contribution of de novo mutations to severe structural malformations diagnosed prenatally using ultrasound. These malformations include heart, CNS, renal and GI abnormalities. In this pilot project we aim to exome sequence 30 parent-foetus trios to ~50X mean coverage and identify de novo functional variants using an algorithm developed in the Hurles group

  Study EGAS00001000167

• Whole exome sequencing data of patients with resectable esophageal adenocarcinoma treated with neoadjuvant atezolizumab and chemoradiation (PERFECT)

  Whole exome sequencing was performed on matched tumor and normal DNA of patients with resectable esophageal adenocarcinoma that particpated in the PERFECT trial. The PERFECT trial is an open-label, single-arm, multicenter, phase II feasibility study (NCT03087864) investigating the safety and efficacy of atezolizumab, combined with neoadjuvant chemoradiotherapy and subsequent esophagectomy.

  Study EGAS00001006504

• Loss of RREB1 in pancreatic beta cells reduces cellular insulin content and affects endocrine cell gene expression

  Genome-wide studies have uncovered multiple independent signals at the RREB1 locus associated with altered type 2 diabetes risk and related glycemic traits. However, little is known about the function of the zinc finger transcription factor RREB1 in glucose homeostasis or how changes in its expression and/or function influences diabetes risk.

  Study EGAS00001006314

• Single-cell atlas of > 1.5 million PBMC with multi-layer omics data in Japanese

  Osaka Atlas of Immune Cells (OASIS) is multi-omics immune cell atlas from 235 Japanese including COVID-19 patients and healthy subjects. The 5’ single-cell transcriptomics data profiled over 1,500,000 peripheral blood mononuclear cells (PBMCs). OASIS links these single-cell transcriptomics data with host genetics, plasma proteomics, and metagenomics data.

  Study EGAS00001008016

• Fecal Microbiota Transplantation for refractory immune checkpoint inhibitor-associated colitis

  We report the first case series of ICI associated colitis successfully treated with fecal microbiota transplantation (FMT), with reconstitution of the gut microbiome and a relative increase in the proportion of regulatory T cells (Tregs) within the colonic mucosa. These preliminary data provide evidence that modulation of the gut microbiome may abrogate ICI-associated colitis.

  Study EGAS00001003217

• Dataset of the transcriptomic profiling of skin biopsies from 221 psoriasis patients following treatment with Zasocitinib

  This dataset contains the paired fastq files generated from 221 samples collected from patients with moderate-to-severe plaque psoriasis and sequenced on the Illumina NovaSeq 6000 platform. Patients were randomized in a 1:1:1:1:1 ratio to receive oral Zasocitinib at doses of 2 mg, 5 mg, 15 mg, 30 mg, or placebo once daily for 12 weeks. Clinical response was defined as achieving a PASI 75 response at week 12, while histologic response was defined as the absence of KRT16-positive cells in lesional skin after 12 weeks of treatment.

  Dataset EGAD50000002224

• Amplicon based re-sequencing of multi-region PDAC samples

  Multi-region tumor samples were cut from frozen sections or FFPEs and reviewed from microdissection and H&E staining in order to select ones with high cellularity. DNA extraction was done using DNeasy Blood & Tissue Kits for frozen samples following the manufacturer’s guideline. Extracted DNAs were processed on an Illumina HiSeq 2500 in a paired end mode (100x100) using a custom targeted panel based on the list of all unique somatic mutations from the original WES data by the Integrated Genomics Operation (IGO) at Memorial Sloan Kettering Cancer Center (New York, NY).

  Dataset EGAD50000000354

• Neonatal and adult recent thymic emigrants produce IL-8 and express complement receptors CR1 and CR2

  By differential gene expression analysis followed by protein expression and functional studies, we define that the naive T cells having divided the least since thymic emigration express complement receptors (CR1 and CR2) known to bind complement C3b- and C3d-decorated microbial products and, following activation, produce IL-8 (CXCL8), a major chemoattractant for neutrophils in bacterial defense. We also observed an IL-8–producing memory T cell subpopulation coexpressing CR1 and CR2 and with a gene expression signature resembling that of RTEs. JCI Insight. 2017;2(16):e93739. https://doi.org/10.1172/jci.insight.93739

  Dataset EGAD00001003793

• TMD-AMKL targeted follow-up

  Genomic libraries will be generated from total genomic DNA derived from 200+ patients with childhood Transient Myeloproliferative Disorder (TMD) and or Acute Megakaryocytic Leukemia (AMKL) as well some matched constitutional samples (n < 50 ). Libraries will be enriched for a selected panel of genes using a bespoke pulldown protocol. 96 Samples will be individually barcoded and subjected to up to two lanes of Illumina HiSeq. Paired reads will be mapped to build 37 of the human reference genome to facilitate the characterisation of known gene mutations in cancer as well as the validation of potentially novel variants identified by prior exome sequencing.

  Dataset EGAD00001000783

• Lymphocyte LCM WGS (2020-02-20)

  Using whole genome sequencing of lymphocytes excised from human tissue using laser capture microscopy (LCM), we identify the mutations arising in these microenvironments. This work will contribute towards developing a catalogue of mutations present in tissue resident lymphocytes across a range of tissues, and will characterize the mutational signatures that result from each microenvironment. . This dataset contains all the data available for this study on 2020-02-20.

  Dataset EGAD00001005992

• Whole genome sequencing data for Molecular Characterization of ETMRs

  This dataset contains whole genome sequencing data from 59 samples. WGS libraries were prepared using the Illumina TruSeq Nano DNA LT Library Prep or TruSeq Nano DNA HT Library Prep Kit following the manufacturer’s instructions. In brief, 100 ng of genomic DNA was fragmented to approximately 350 bp using a Covaris ultrasonicator (Covaris). The fragmented DNA was then end-repaired, size-selected using magnetic beads, extended with an ‘A’ base on the 3′ end and ligated with TruSeq paired-end indexing adapters. Up to four lanes per sample have been sequenced resulting in 222 Fastq files (paired end).

  Dataset EGAD00001006211

• Multi-region RNA-Seq data of 10 neuroblastoma cases

  To investigate intratumour heterogeneity and to better understand tumour evolution in neuroblastoma, we have performed a multi-region RNA sequencing on a total of 51 spatially separated tumor samples from 9 primary neuroblastomas (2 low-risk, 1 intermediate-risk and 6 high-risk) and 1 relapsed neuroblastoma. We also assessed the impact of chemotherapy on the clonal expansion by sequencing tumour regions from one medium risk and one high-risk tumour for which we had matched samples obtained at diagnosis and after chemotherapy.

  Dataset EGAD00001008133

• Embryonic tumour transmission in monozygotic twins

  We have a case of two siblings (twins) who were born with nodular blue rashes over their body. The first twin had a large periorbital subcutaneous mass which was diagnosed as infantile undifferentiated sarcoma. This baby was too systematically unwell for chemotherapy and died at 12 days of age. The second sibling received two cycles of emergency chemotherapy however died due to disease progression and secondary haemorrhage at 2 months of age. Post-mortem normal and tumour samples have been taken. In addition to placental tissue and parental germline DNA, the goal will be to investigate intra-uterine transfer of sarcoma and the phylogenetic relationship of tumours in both twins.

  Dataset EGAD00001015681

• UM

  metabolite levels provided by UM platform (Creative Dynamics Inc, NY, USA) (the data is raw abundance. Mapping was applied on log10 transformed data)

  Dataset EGAD00010002146

• Multimodal Profiling of 500,000 Memory T Cells from a Tuberculosis Cohort Identifies Cell State Associations with Demographics, Environment, and Disease

  We conducted CITE-seq to measure whole transcriptome gene expression and surface expression of 31 proteins. We assayed >500K memory T cells from 259 donors from a tuberculosis progression cohort (128 cases: former progressors and 131 controls: non-progresssors/latent infection) >4 years post-infection after returning to immune steady state. We defined 31 memory T cell states influenced by age, sex, genetic ancestry, and season. After correcting for these covariates, we found that one cell state (C-12), resembling the T helper cells Th17s, were depleted in cases compared to controls. When sorted ex vivo, this state responds to polyclonal or Mycobacterium tuberculosis (Mtb) peptide antigen stimulation with interleukin-17 (IL-17) or interferon gamma (IFNg).

  Study phs002467

• TCR- and BCR-sequencing data for The interface of malignant and immunologic clonal dynamics in high-grade serous ovarian cancer

  Each tumor sample was cut into three pieces, yielding two end-pieces for cryovials and a middle portion placed in 10% buffered formalin. End pieces were homogenized manually and with a paddle blender (Stomacher). All paraffin-embedded blocks, including formalin-fixed tumor samples and molecular-fixed fallopian tubes, were sectioned and stained with hematoxylin and eosin prior to expert histopathological review to confirm the presence of high grade serous carcinoma. Homogenized end pieces were then flash frozen, and RNA was extracted using the miRNeasy Mini kit. Nanodrop was used to assess quality (260/280) and quantity. Total RNA samples were also QC checked using the Caliper HT RNA HiSens assay. Samples ranging from 60-255ng RNA were re-arrayed into a 96-well plate. 5'-RACE PCR was carried out as described in "The interface of malignant and immunologic clonal dynamics in high-grade serous ovarian cancer" (Zhang et al.). Briefly, this involved first round and nested PCR with TRB (TCR beta chain) and IGH (immunoglobulin heavy chain) gene-specific primers. The indexed libraries were sequenced on the Illumina HiSeq platform with paired-end 250bp reads using v2 chemistry reagents.

  Dataset EGAD00001003985

• PDAC clinical phenotype data with CA19-9 and Lewis antigen status

  This dataset contains individual-level clinical phenotype data from patients with pancreatic ductal adenocarcinoma, including CA19-9 measurements, Lewis antigen status, and relevant clinicopathological variables. Data were generated as part of an ethically approved study and are available under controlled access.

  Dataset EGAD50000002254

• 5WGS and 35WES sample pairs belongs to COCA-CN

  There are 5WGS and 35WES sample pairs from the first affiliated hospital of kunming medical university, which belongs to ICGC projects COCA-CN.

  Dataset EGAD00001003456

• Whole genome shotgun sequencing and somatic mutations data in Hepatocellular carcinoma

  There are 88 paired samples from HCC patients including tumors and matched adjacent normal tissues which were sequencing by Illumina HiSeq 2000 platform.

  Dataset EGAD00001003760

• Whole genome sequencing data from whole genome amplified single cells and unamplified bulk samples

  The dataset includes paired end fastq files of whole genome sequencing data on the Illumina platfrom. Individual samples are multiple annealing and looping based amplified single fibroblasts and multiple displacement amplified single T lympocytes, including unamplified bulk samples.

  Dataset EGAD00001004195

• 200PG : WGS Raw Sequence (fastq)

  200PG : WGS Raw Sequence (fastq) : Raw WG sequence data (fastq) in this dataset are from the 124 CPCGene Tumour/Normal Pairs used in the 200PG Study. https://www.ncbi.nlm.nih.gov/pubmed/28068672

  Dataset EGAD00001001094

• Human tumor bulk RNA-seq

  We profiled 186 patient tumor samples by bulk RNA-seq. These includes 38 embryonal brain tumors, 101 high-grade gliomas, 24 low-grade gliomas, 10 medulloblastoma and 13 matched normals. The raw fastqs are provided.

  Dataset EGAD00001005131

• RNA-seq cohort of normal weight women

  RNA-seq data of non-tumorous breast tissue. There are 32 samples in this cohort.

  Dataset EGAD00001007073

• Single cell TCR Analysis of regulatory Tcells from blood, fat and skin

  Regulatory Tcells were FACS sorted and processed with 10x Genomics Chromium Next GEM SingleCell V(D)J Reagents Kits v1.1 sequencing. In total 17 samples were processed. Fastq files are supplied.

  Dataset EGAD00001007661

• Copy number profiling of tissue and plasma samples from high grade serous epithelial ovarian cancer patients

  This dataset includes 289 samples from 46 high grade serous epithelial ovarian cancer patients. Data are from both tissue samples (either primary tumor, or synchronous metastases) and circulating cell-free DNA (cfDNA) of plasma samples taken during therapy and follow-up.

  Dataset EGAD00001006422

• 4C-seq in endometrial healthy and tumor tissues

  4C-seq performed on 10 slices (30um thick) of fresh frozen endometrial tissues. These tissue include 2 healthy tissues and 4 tumor tisseus (post-menopausal patients) in replicate. The library has been performed using DpnII (primary) and NlaIII (secondary) restriction enzymes. Raw single-end fastq.gz files are provided.

  Dataset EGAD00001010897

• Targeted_replication_of_LVOTO_genes

  Non-syndromic cases of congenital heart defects (CHD) exhibit variable modes of inheritance (Mendelian and non-Mendelian). Several studies have identified strong candidates in humans by taking a candidate gene approach as well as by using whole exome next generation sequencing (NGS). So far these studies could only explain a minor fraction of the observed phenotype in humans, most of them in syndromic cases and no single study has focused on the subset of cases with left ventricular outflow tract obstruction (LVOTO). To discover novel disease-causing genes a large cohort of patients with LVOTO, approximately 100 cases, 25 families and 100 trios have been exome sequenced. This study based on NGS sequencing data yielded several known and novel compelling candidate genes, such as MYH6, NR2F2 and MYH11, but also novel ones, such as ITGB4. To evaluate the significance of our findings in a replication cohort we assembled another 1614 cases with an LVOTO phenotype from our collaborators in Toronto, Berlin and Amsterdam. Targeted resequencing in this additional cohort will help to find additional cases with mutations in the identified candidate genes to strengthen genotype-phenotype association. We will use control data from the INTERVAL project for case/control analyses The pulldowns will be performed as 24-plex ISC with 192 or greater indexes, and the sequencing will be performed with 192 samples per lane, requiring 9 lanes of sequencing.

  Study EGAS00001001238

• Therapeutic Resistance to PI3K-alpha Inhibitors

  We have studied the tumor genomic evolution in a patient with metastatic breast cancer bearing an activating PIK3CA mutation. The patient was treated with the PI3Kα inhibitor BYL719 and achieved a lasting clinical response on BYL719, but eventually progressed to treatment and died shortly thereafter. A rapid autopsy was performed and a total of 14 metastatic lesions were collected for further analysis. In order to identify possible genetic determinants of acquired resistance to PI3Kα inhibition, we took a three-step approach. First, we examined both the primary tumor (before BYL719 treatment) and the new lung metastasis by whole genome sequencing (DNA from the spleen was used as a normal control). Then, we analyzed the primary tumor, lung metastasis, and the peri-aortic lesion that remained stable (responding) at the time of progression to BYL719 therapy by whole exome sequencing. Finally, to confirm and expand our findings, we sequenced the primary tumor and all the metastatic lesions to >500-fold coverage using a custom targeted deep-sequencing assay, MSK-IMPACT. Using this 3-step approach, we have demonstrated that patient’s lesion underwent parallel genetic evolution at multiple metastatic sites with different PTEN genomic alterations leading to a convergent PTEN- null phenotype resistant to PI3Kα inhibition. In order to expand our observations, we analyzed paired samples (pre-treatment and at progression) from six additional patients enrolled in the BYL719 trial. Acquired bi-allelic loss of PTEN was found in one additional patient treated with BYL719 whereas in two patients PIK3CA mutations present in the primary tumor were no longer detected at the time of progression. To functionally characterize our findings, inducible PTEN knockdown in sensitive cells resulted in resistance to BYL719, while simultaneous PI3K-p110β blockade reverted this resistance phenotype, both in cell lines and in PTEN-null xenografts derived from our patient. We conclude that parallel genetic evolution of separate sites with different PTEN genomic alterations leads to a convergent PTEN-null phenotype resistant to PI3Kα inhibition.

  Study EGAS00001000991

• Caregiving as a Natural Stressor in Studies of the Role of Genes That Affect Serotonin Function in Regulating Risk Factors for Coronary Heart Disease (CAREGIVER)

  The burden of caregiving for an ill relative has been shown to interact with existing comorbidities to increase risk of several health outcomes including metabolic syndrome and blood pressure reactivity. The CAREGIVER study was developed to compare cardiometabolic risk factors in caregivers and controls. These risk factors include physiologic measures, psychologic measures, neighborhood characteristics, and genetic and genomic factors. DNA and plasma were collected and used for examination of cardiometabolic and stress biomarkers, genotyping and methylation analysis.

  Study phs001747

• Somatic mutations and clonal dynamics in healthy and cirrhotic human liver

  Chronic liver injury predisposes to cirrhosis and hepatocellular carcinoma, but how somatic mutations accumulate in liver disease is unexplored. We sequenced whole genomes of 400 microdissections of 100-500 hepatocytes from 5 normal and 6 cirrhotic livers. Compared to normal liver, cirrhotic liver had higher mutation burden, especially structural variants, including chromothripsis. Cirrhotic nodules were oligoclonal; sometimes entirely derived from a single, recent common ancestor. Clonal expansions millimeters in diameter occurred in cirrhosis in the absence of known driver mutations. Endogenous mutational processes predominated, although signatures of polycyclic aromatic hydrocarbon and aristolochic acid exposure occurred in some samples. Up to 10-fold within-patient variation in activity of exogenous signatures existed between adjacent cirrhotic nodules, with both clone-specific and microenvironmental forces shaping this heterogeneity. Synchronous hepatocellular carcinomas drew from the same repertoire of mutational signatures as background cirrhotic liver, but with higher burden. Somatic mutations chronicle the exposures, toxicity, regeneration and clonal structure of liver tissue as it progresses from health to disease.

  Dataset EGAD00001004578

• DAC for Breast Invasive Lobular Carcinoma CDH1 study

  We developed an artificial intelligence (AI)-model applied to histological images trained using CDH1 biallelic mutations, pathognomonic for breast invasive lobular carcinoma (ILC), as ground truth. We evaluated the performance of the AI-model to predict the presence of CDH1 biallelic mutations and to diagnose ILC. Subsequently, we investigated the molecular underpinning of cases predicted by the model to harbor a CDH1 biallelic mutations but lacking these alterations according to targeted sequencing. We then subjected one ILC lacking CDH1 biallelic mutations and lacking CDH1 promoter methylation to whole genome sequencing (WGS) to determine the molecular basis of its lobular phenotype.

  Dac EGAC50000000333

• snRNA-seq schizophrenia control Prefrontal cortex

  Human Brodmann Area 8/9 tissue from 43 schizophrenia subjects and 42 control individuals was obtained from three sources, NBB (Netherlands Brain Bank), Craig A. Stockmeier (University of Mississippi Medical Center), Macedonian/New York State Psychiatric Institute Brain Collection (Andrew J. Dwork, Columbia University). All subjects included in the study were matched between the two groups for age, gender, and postmortem interval. Nuclei were isolated and enriched for 85% neuronal nuclei before single nucleus RNA sequencing was performed with 10x Genomics Chromium Single Cell protocol v3.

  Dataset EGAD50000002447

• SATB1 KO Treg and Teff cells: ATAC-seq

  We expanded human Treg and CD4+ Teff cells for 9 days, re-activated the cells and performed CRISPR/Cas9 RNP-mediated KO at day 11. The cells were treated with a pro-inflammatory cytokine IL-12 on day 12. 4 days after editing, living cells were FACS-sorted, the cell nuclei were extracted and prepared for ATAC-seq. AAVS1 KO served as control. The transcription factors SATB1 and two other targets (included to increase the robustness of the dataset) were knocked-out. Three biological replicates have been applied.

  Dataset EGAD50000001276

• SATB1 KO Treg and Teff cells: RNA-seq

  We expanded human Treg and CD4+ Teff cells for 9 days, re-activated the cells and performed CRISPR/Cas9 RNP-mediated KO at day 11. The cells were treated with a pro-inflammatory cytokine IL-12 on day 12. 4 days after editing, living cells were FACS-sorted, the RNA was extracted and prepared for RNA-seq. AAVS1 KO served as control. The transcription factors SATB1 and two other targets (included to increase the robustness of the dataset) were knocked-out. Three biological replicates have been applied.

  Dataset EGAD50000001277

• Chromatin profiling of baseline and Notch inhibitor treated HCC PDX model

  We generated chromatin accessibility profiles for anti-Notch2 (n=3) and anti-gD (n=3) treated LIV78 tumors. Tumors were isolated, snap frozen in liquid nitrogen and stored at -80C. Tumor tissue was pulverized using a Covaris CP02 CryoPrep Pulverizer. Flash frozen pulverized tumor samples were sent to Active Motif to perform the ATAC-seq assay. Resulting material was quantified using the KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems), and sequenced with PE42 sequencing on the NextSeq 500 sequencer (Illumina) to produce FASTQ sequencing files.

  Dataset EGAD50000000735

• Perturb-seq dataset

  We performed a systematic, genome-wide investigation of enhancer regions in colorectal cancer (CRC). We identified 12,117 putative enhancer regions using H3K27ac and H3Kme1 ChIP-seq and ATAC-seq. We performed scRNA-seq in HT29 and SW480 (MSS CRC cell lines) using the Parse Biosciences WT-mega kit with CRISPRi/dCas9 inhibition of these regions (Perturb-seq). The Parse split-pipe pipeline was used to demultiplex the raw fastq files into the processed files (mtx files for genes and gRNA) for each cell line.

  Dataset EGAD50000000375

• Blueprint: A human variation panel of genetic influences on epigenomes and transcriptomes in three immune cell types, (ChIP-Seq for mature neutrophil, on genome GRCh37)

  ChIP-Seq data for 182 mature neutrophil sample(s). 2847 run(s), 366 experiment(s), 355 analysis(s) on human genome GRCh37. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/blueprint_Epivar/protocols/README_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002670

• Blueprint: A human variation panel of genetic influences on epigenomes and transcriptomes in three immune cell types, (RNA-Seq for mature neutrophil, on genome GRCh37)

  RNA-Seq data for 205 mature neutrophil sample(s). 205 run(s), 205 experiment(s), 205 analysis(s) on human genome GRCh37. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/blueprint_Epivar/protocols/README_rnaseq_analysis_sanger_20160816

  Dataset EGAD00001002675

• The identification of genetic vulnerabilities in head and neck cancers for the development of novel therapies (2020-01-15)

  CRISPR/Cas9 lethality screens in a set of Asian head and neck cancer cell lines to identify novel targets. . This dataset contains all the data available for this study on 2020-01-15.

  Dataset EGAD00001005784

• 252 human breast cancer samples in WGS and WES

  We analyzed chromothripsis in 252 human breast cancers from two patient cohorts (149 metastatic breast cancers, 63 untreated primary tumors, 29 local relapses, 11 longitudinal pairs) using whole-genome and whole-exome (paired) sequencing. A lot of the WGS samples were sequenced on Illumina HiSeq X-Ten using Illumina TruSeq Nano DNA. For exome sequencing Agilent_SureSelect_V5+UTRs has been used (sequencing on Hiseq2000, Hiseq2500 and Hiseq4000). For exome sequencing Agilent_SureSelect_V5+UTRs has been used (sequencing on Hiseq2000, Hiseq2500 and Hiseq4000).

  Dataset EGAD00001007563

• This committee is composed on individuals who have access to the data corresponding to this project: Gut microbiome modulates response to anti PD-1 immunotherapy in melanoma patients

  Dac EGAC00001000758