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• Illumina GSA-MD v3 genotyping arrays for 183 samples

  Genotyping arrays for 183 samples from patients with a neuroendocrine tumor of the small intestine. All samples have been hybridized on Illumina GSA-MD v3 arrays with standard automated protocols. Reading of the chips was performed on Illumina iScan+ scanners and this file is the result of primary analysis done using Illumina GenomeStudio software. It contains data for 147 tumors, 2 adenomas, 1 lymph node, 19 mesenteric nodules, 6 liver metastasis and 8 normal ileum samples.

  Dataset EGAD50000000905

• Transcriptome sequencing of neuroendocrine tumors of the small intestine

  This dataset contains 206 RNASeq samples from a cohort of patients with neuroendocrine tumors of the small intestine. Libraries were prepared using a Illumina TruSeq Stranded mRNA kit following the manufacturer’s recommendations. Sequencing was performed on Illumina Novaseq6000 machine with a 2x75bp paired-end fashion. This dataset contains data for 169 tumors, 22 mesenteric nodules, 8 liver metastases, 2 adenomas, 1 lymph node and 4 normal ileum samples.

  Dataset EGAD50000000906

• The BEACCON study: tumour sequencing

  This dataset consists of paired-end DNA sequencing (whole exome and targeted-capture) of tumours for the BEACCON study. There are 240 unique samples consisting of 92 matched tumour-germline pairs and 56 unmatched tumours totalling 148 patients. There are 33 paired and 6 unpaired tumours sequenced using the Agilent SureSelect All Human Exon v6 libraries, 1 paired and 8 unpaired tumours sequenced using Agilent SureSelect All Human Exon v7 libraries and 48 paired and 3 unpaired tumours sequenced using Twist Bioscience Comprehensive Human Exome v1 libraries totalling 176 whole exome samples. There are 3 paired and 58 unpaired tumours sequenced using a custom Agilent SureSelectXT library totalling 64 targeted capture samples.

  Dataset EGAD00001009299

• Genomic Characterization of HPV+ Oropharyngeal Tumors

  Archived surgical samples from HPV positive oropharynx patients were identified and sequenced through the UNC/UTHSC NCTN Integrated Translational Science Center. DNA targeted panel sequencing data will be available through dbGaP.

  Study phs003925

• Waldenström Macroglobulinemia Single-Cell Data Access Committee

  This Data Access Committee (DAC) is responsible for reviewing and approving access requests for controlled-access human single-cell sequencing data, including single-cell RNA sequencing and immune receptor profiling, generated from patients with Waldenström macroglobulinemia. The DAC ensures that all data access requests comply with the informed consent provided by study participants and are consistent with applicable ethical and regulatory requirements.

  Dac EGAC50000000863

• Paired RNA sequencing of Thymic epithelial tumors - Additional Dataset

  Paired RNA sequencing of additional samples of Thymic epithelial tumors. Uploaded are the paired fastq files, sequencers were Illumina HiSeq 2500, HiSeq 4000, NovaSeq 6000 and HiSeq X Ten. The kits used were Illumina Truseq RNA and Illumina Truseq stranded mRNA.

  Dataset EGAD50000000324

• Whole exome Sequencing (WES) of multiple tumor biopsies, patient-derived spheroids and leukocyte DNA from colorectal cancer patients (BAM files)

  WES was performed using the KAPA-Hyper prep kit from Illumina (Roche, Basel, Switzerland) for library construction, followed by exome capture using Niblegen SeqCap EZ Human Exome Library v3.0 (Roche). Reads were mapped using BWA MEM against the humane reference genome HG19.

  Dataset EGAD00001003821

• Single cell RNA sequencing of colorectal cancer patients (CRC-SG1)

  Fresh single-cell suspensions were loaded into the Chromium system (10x Genomics) targeting 5,000 cells per well. Barcoded sequencing libraries were generated using 3’v3 Reagent kit.

  Study EGAS00001006013

• sQTL summary statistics

  This dataset contains the sQTL summary statistics (nominal pass, significant sQTLs). sQTL mapping was performed with QTLtools. This dataset was generated as part of the following study: Panousis et al (2019). Combined genetic and transcriptome analysis of patients with SLE: Distinct, targetable signatures for susceptibility and severity.

  Dataset EGAD00001005042

• DNA methylation and Metabolic data from type 2 diabetes adolescents

  This data contains DNA methylation data obtained from the PBMCs obtained from type 2 diabetes adolescents and controls. There are 21 diabetic samples and 10 controls. This dataset also contains metabolic data obtained from the serum of 155 samples. There are 113 diabetic and 42 control samples.

  Dataset EGAD00001005271

• Exome_pituitary_adenoma

  Whole‐exome sequencing was performed using NimbleGen MedExome capture (Roche NimbleGen, Madison, WI, USA) from 1 μg of high quality genomic DNA, followed by sequencing of libraries using paired-end mode (2x 75bp) on a Nextseq 500 platform (Illumina, San Diego, CA, USA), at the Genomics Platform of the Cochin Institute. Reads were aligned on hg19 (GRCh37) using BWA V0.7.17.

  Dataset EGAD00001004997

• Human brain development single cell sequencing

  379 tissue samples from various parts of the developing human embryo brain were dissociated and single cells were collected and processed without bias for mRNA-seq using 10X chromium 3' protocol. Libraries were sequenced on Illumina NovaSeq and reads aligned against the human GRCh38 genome.

  Dataset EGAD00001006049

• Single-cell RNA sequencing of acute myeloid leukemia patients

  Single-cell RNA sequencing was performed on bone marrow mononuclear cells from 8 acute myeloid leukemia patients at diagnosis. The profiling was performed using 10x Genomics 3' (5 samples) and 5' (3 samples) platforms. The raw data are available as fastq files.

  Dataset EGAD00001006173

• Patient-tailored design for selective co-inhibition of leukemic cell subpopulations

  Single-cell RNA sequencing was performed on bone marrow mononuclear cells of 2 acute myeloid leukemia patients at refractory stage. The profiling was performed using 10x Genomics Chromium Single Cell 3ʹ Gene Expression platform. The raw data are available as fastq files.

  Dataset EGAD00001006360

• RNA-seq TPM matrices

  Matrices of TPM-normalized counts from RNAseq data for the three phase II clinical trials (IMvigor210, POPLAR, IMmotion150) and the phase I clinical trial PCD4989g.

  Dataset EGAD00001006741

• WES Melanoma subtypes

  The dataset include sequencing data from 23 patients diagnosed with metastatic melanoma. The 23 metastatic melanoma subtypes consisted of cutaneous melanoma (CM, n=10); head and neck melanoma (HNM, n=7); uveal melanoma (UM, n=4); acral lentiginous (AM, n=1) and mucosal melanoma (MM, n=1).

  Dataset EGAD00001008336

• Single cell RNA-sequencing of treatment naïve PDAC patient samples

  Single cell RNA-sequencing of treatment naïve PDAC patient samples. We have 10 samples, sequenced using the 10X genomics chromium platform with 3 prime chemistry. We are submitting FASTQ files representing the index files (I1), Read1 (R1) and Read2 (R2).

  Dataset EGAD00001008961

• Human Hi-C

  This dataset contains 2 human tumor-derived cell lines and 1 human tumor Hi-C samples. The raw fastq files and the processed .hic file is provided for each sample.

  Dataset EGAD00001009050

• RNAseq of jejunum (small intestine) harvested from CDAHFD mice treated for 8 weeks with either the MGAT2 inhibitor compound BMS-963272 or vehicle

  This experiment consists of RNAseq of jejunum (small intestine) harvested from CDAHFD mice treated for 8 weeks with either the MGAT2 inhibitor compound BMS-963272 (N = 14) or with vehicle (N = 14).

  Dataset EGAD00001009390

• Single cell epigenomic study of H3-K27M mutant diffuse midline glioma across age and location

  This dataset contains the open chromatin profiles of 8 patient H3-K27M mutant DMGs utilizing the single-cell/nucleus assay for transposase-accessible chromatin using sequencing (snATAC-seq)

  Dataset EGAD00001010170

• Analyses of RNAseq data from NEN patient derived tumor organoids (PDTOs) and matched parental tumors

  The dataset includes RNA-seq expression R data, RNA-seq gene counts matrix, and RNA-seq gene FPKM matrix from 21 NEN tumors or metastases and matched PDTOs. The sequencing was done with either a Nextseq 2000 or a NovaSeq 6000 instrument.

  Dataset EGAD00001009994

• Paired RNA-Seq of Tumor Organoids from glioblastoma, 2 patients, treated with different small molecule inhibitors

  Tumor Organoids from glioblastoma, 2 patients, treated with different small molecule inhibitors. Paired RNA-Seq was done on NovaSeq 6000 with the Illumina TruSeq stranded mRNA Kit. The small inhibitors GW2580, BLZ945 and PLX3397 were used. DMSO was used as control.

  Dataset EGAD00001011274

• Single-Cell Mitochondrial Variant Profiling via TAMITO-seq

  This dataset focuses on mitochondrial variant detection using the TAMITO-seq protocol. A pre-designed mitochondrial panel (https://designer.missionbio.com/catalogpanels/Virtual-mtDNA) was spiked into the scTAMseq workflow targeting 200 CpGs and 167 genotyping loci. Data were generated from a peripheral blood sample of a healthy donor, donor X.2, multiplexed with data from another donor.

  Dataset EGAD00001015494

• The ACS study

  Dac EGAC00001002140

• The Druze Analysis Group

  Dac EGAC00001000215

• The PREDO Study DAC

  Dac EGAC00001000511

• DAC Wachten Laboratory and Toma Laboratory, University of Bonn/University Hospital Bonn

  DAC for collaborative projects of the Wachten Laboratory (Institute of Innate Immunity, University of Bonn, University Hospital Bonn) and the Toma Laboratory (Institute of Pathology, University Hospital Bonn). Contact: Prof. Dr. Dagmar Wachten dwachten@uni-bonn.de Institute of Innate Immunity, University Hospital Bonn, University of Bonn, Germany Prof. Dr. Marieta I. Toma Marieta.Toma@ukbonn.de Institute of Pathology, University Hospital Bonn, Germany

  Dac EGAC50000000916

• Whole-exome sequencing data from breast cancer recurrence, endometrial cancer, and colon tumor samples harboring a rare germline BARD1 variant

  This dataset comprises whole-exome sequencing data from tumor and matched blood samples of a patient with breast cancer recurrence and endometrial cancer carrying a germline BARD1 p.(Gly753Val) variant, as well as from the colon tumor of the proband's father

  Dataset EGAD50000002412

• DCIS_FF_RNAseq

  This RNAseq dataset contains full transcriptome data on n=77 pure DCIS samples. The RNA is derived from fresh-frozen DCIS samples, obtained from two hospital based cohorts (NKI cohort and Oslo cohort). The libraries were sequenced with 54 bp paired end reads using a Novaseq instrument (Illumina). We share fastq data files of paired end sequencing (two files per sample).

  Dataset EGAD50000002123

• Whole exome sequencing data of matched pairs of primary tumour and normal frozen tissue of seven osteosarcoma patients

  This dataset contains whole exome sequencing data of matched pairs of primary tumour and normal frozen tissue of seven osteosarcoma patients. Whole exome sequencing with a minimum coverage of 100x was performed using the Illumina Novaseq6000 platform and the Agilent SureSelect Human All Exon V7 kit.

  Dataset EGAD50000002264

• Whole exome RNA sequencing of FFPE material from 49 pediatric BCP-LBL patients.

  This study contain the results of whole exome-targeted transcriptome analyses of FFPE material from 49 pediatric B-cell precursor lymphoblastic lymphoma patients. Data are provided as Fastq files.

  Study EGAS50000000289

• Whole_Exome_sequencing_in_a_large_IBD_pedigree

  We perform whole exome sequencing on samples from a large IBD pedigree. The selected samples are from more distantly related family members (healthy and with IBD) and a set of matched population (Ashkenazy Jewish ancestry) samples.

  Study EGAS00001000240

• Whole genome sequencing, SNP array and RNA-seq of uveal melanomas

  We conducted whole genome sequencing and DNA SNP array of 12 uveal melanoma genomes and their matched DNA from blood. We also conducted RNA-seq of the 12 tumour samples.

  Study EGAS00001000472

• Von Hippel-Lindau syndrome multi-region exome sequencing project from two patients undertaken at Cancer Research UK's London Research Institute

  Multi-region whole exome sequencing of tumours from patients with Von Hippel-Lindau syndrome reveals convergence of mutayional events upon the PI3L-AKT-mTOR signalling pathway.

  Study EGAS00001000907

• Gene panel sequencing of paired samples from primary and relapsed IDH-wt glioblastomas

  This dataset contains gene panel sequencing data from 43 sample pairs of primary and relapsed IDH-wt glioblastomas. The gene panel covers 50 glioma-associated genes. 14 of the sequenced sample pairs were sequenced with whole genome sequencing also and are accessible under EGAD00001004563.

  Dataset EGAD00001004565

• ICR Exome Optimization series

  Exome sequencing of 142 samples with corresponding Sanger sequencing results for 416 variants and 288 negative sites. DNA library preps prepared with Illumina TruSeq sample preparation kit. The captured DNA libraries were PCR amplified using the supplied paired-end PCR primers. Sequencing was performed with an Illumina HiSeq2000 (SBS Kit v3, one pool per lane) generating 2x101-bp reads.

  Dataset EGAD00001001462

• Exome sequencing of 277 rainforest hunter-gatherers and neighbouring farmers from Central Africa

  Exome sequencing of 277 rainforest hunter-gatherers (RHG) and neighbouring farmers (AGR) from Central Africa was performed based on the Nextera Rapid Capture Expanded Exome Kit (62-Mb content) with the Illumina HiSeq 2500. After QC filters, exomes of 266 unrelated individuals were obtained at high coverage (Lopez et al., Curr Biol 2019).

  Dataset EGAD00001005138

• Human tumor single-cell

  We profiled 11 patient tumor samples by single-cell and single-nuclei RNA-seq using 10X Chromium 3'. These include samples from the following entities: WNT-subtype medulloblastoma (N=3), embryonal tumors with multilayered rosettes (N=3), and atypical teratoid-rhabdoid tumors (N=5). The BAM files are provided.

  Dataset EGAD00001005129

• Human tumour ChIP-seq.

  We profiled 16 patient tumour samples by ChIP-seq. H3K27ac and Input are provided for 16 samples and H3K27me3 is provided for 14 samples. Among the 16 samples, 9 are G34WT and 7 are G34R/V. The raw fastq or bam files are provided.

  Dataset EGAD00001006100

• Whole exome sequencing of long-term, never relapse exceptional responders of trastuzumab-treated HER2+ metastatic breast cancer

  The dataset contains Whole Exome Sequencing data (BAM files) of 22 samples from HER2+ metastatic breast patients. For 9 of the 13 tumours samples there are paired controls available from normal tissue. There are 8 tumours samples that are from treatment-responder patients and 5 tumours samples from non responder patients.

  Dataset EGAD00001006217

• Illumina 5'end RNA sequencing

  The dataset contains 200 fastq files of Illumina 5'end RNA sequencing data of 50 PBMC samples. The paired-end data includes 100 fastq files (R1 and R2) of 50 full-length cDNA sequencing libraries and 100 fastq files (R1 and R2) of 50 HLA amplicon sequencing libraries.

  Dataset EGAD00001006838

• He et al. RNA-seq data

  This dataset are the bam files of RNA-seq data from the paper by He et al.

  Dataset EGAD00001007135

• INS01: Targeted sequencing of four tumours from a suspected VHL patient

  This dataset contains fastq files from four tumours that underwent targeted sequencing on panel for suspected VHL disease. The samples contained within the dataset and their corresponding sample ID are: ccRCC - M19-12422, Pheochromocytoma - M19-13800, Expelled lung tissue- M19-13801, and Liver biopsy- M19-13802.

  Dataset EGAD00001008438

• Metastatic Pediatric Sclerosing Epithelioid Fibrosarcoma

  This dataset contains different samples from a single patient with SEF. The dataset contains whole genome, whole exome and RNAseq information. Two of the DNA sequencing samples also contain matched normals.

  Dataset EGAD00001007516

• Metastatic Pediatric Sclerosing Epithelioid Fibrosarcoma

  This dataset contains different samples from a single patient with SEF. The dataset contains whole genome, whole exome and RNAseq information. Two of the DNA sequencing samples also contain matched normals.

  Dataset EGAD00001007515

• PGDx elio™ tissue complete assay: targeted sequencing analyses of tissue DNA

  The dataset "PGDx elio™ tissue complete assay: targeted sequencing analyses of tissue DNA" includes paired end FASTQ reads of 28 tissue samples from metastatic colorectal cancer patients. Sequencing was performed using a panel consisting of 505 genes, targeting 2,500x depth across the targeted regions.

  Dataset EGAD00001009720

• RNAseq data from NEN patient derived tumor organoids (PDTOs) and matched parental tumors - MUMC

  The dataset includes fastq files from 4 NEN tumors or metastases and matched PDTOs. The sequencing was done with either a Nextseq 2000 or a NovaSeq 6000 instrument.

  Dataset EGAD00001009991

• Bulk BCR NGS data from metastatic breast tumours from donors with therapy-resistant lethal metastatic breast cancer.

  Bulk B Cell Receptor high-throughput sequencing data across 27 metastatic breast tumours obtained from 8 donors with therapy-resistant lethal metastatic breast cancer at the time of a warm autopsy. The 35 samples were sequenced on an Illumina MiSeq instrument and their raw FastQ files deposited here.

  Dataset EGAD00001010023

• DAC of the BriTROC-1 project

  Dac EGAC00001003291

• DAC for the study EGAS00001003572

  Dac EGAC00001001174