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• CD49f single-cell methylomes

  74 CD49f single-cell methylomes are from cord blood of donor1, and 84 from cord blood of donor2. Samples from donor1 have one sequencing lane, and samples from donor2 have five sequencing lanes. This dataset was generated using Post-Bisulfite Adapter Ligation (PBAL), a bisulfite based whole genome protocol. In total this dataset consists of 494 runs.

  Dataset EGAD00001003913

• Single cell analyses of transcriptome and epigenome in neuroblastoma infiltrated bone marrow

  We report transcriptional and genome-wide ATAC-seq analyses at single cell resolution of 16 bone marrow samples with and without neuroblastoma infiltration. Our samples span across several neuroblastoma models, including MYCN amplified, ATRX mutated, and sporadic (lacking either alteration).

  Study EGAS00001006106

• Transcriptomic analysis of TFEB knockdown in LT-HSC.

  Long-term hematopoietic stem cells (LT-HSC) were sorted from human cord blood and cultured overnight before transduction with lentiviral vectors overexpressing an shRNA against Renilla (shCTRL) or TFEB (shTFEB). Six days later, mCherry+ transduced cells were sorted for RNA extraction and sequencing.

  Study EGAS00001004967

• Valid reads

  Valid reads obtained after analyzing in situ Hi-C data of 16 normal B cells (3 naive B cells, 3 germinal center B cells, 3 plasma cells, and 3 memory B cells, together with a merge file for each subpopulation), 7 chronic lymphocytic leukemias (2 unmutated IGHV and 5 mutated IGHV), and 5 mantle cell lymphomas (2 conventional and 3 leukemic non-nodal).

  Dataset EGAD00001006486

• Genomic Analysis of Anaplastic Thyroid Carcinoma

  This dataset includes WGS & WTS alignment data generated from 1 ATC tumor, its matched peripheral blood specimen and 3 authenticated ATC cell lines, THJ-16T, THJ-21T and THJ-29T. In addition, it includes WTS data from extra 4 unique anaplastic cell lines, ACT-1, C643, HTh7 and T238.

  Dataset EGAD00001001321

• 20210303_EGA_Melanoma Garg et al Nat Commun,  2021

  RNAseq of 55 melanoma tumors that were used as a validation dataset in Garg et al Nat Commun,  2021 Feb 18;12(1):1137. doi: 10.1038/s41467-021-21207-2.

  Dataset EGAD00001007055

• ATAC-seq dataset of patient and healthy donors

  ATAC-seq dataset on a patient (P) presenting with defects of immunity and two (C5, C6) healthy donors. This dataset contains raw and processed files from ATAC-seq chromatin accessibility analysis. There are 3 single-read (50 bp) fastq files (1 per patient/ donor). Processed files consist of narrowPeak files (1 per patient/ donor) and one file that contains read counts in consensus peaks.

  Dataset EGAD00001008370

• RNA-seq derived from metastatic Castration-Resistant Prostate Cancer

  Patients with progressive, metastatic castration-resistant prostate cancer (mCRPC) underwent metastatic tumor biopsy. 118 total samples including 14 paired samples (baseline and later progression). Various organ sites including soft tissue & bone were present. Published in DOI: 10.1200/JCO.2017.77.6880 Journal of Clinical Oncology 36, no. 24 (August 20, 2018) 2492-2503.

  Dataset EGAD00001008991

• MSI2 knockdown and inhibition in mantle cell lymphoma cell lines RNAseq data

  Fastq transcriptomic sequencing files from Z138 mantle cell lymphoma (MCL) cell line upon MSI2 knockdown (KD) with two different shRNAs and after MSI2 inhibition with Ro 08-2750 small molecule. Dataset includes 4 samples of Z138 MSI2-KD, 4 of Z138 control, 3 of Z138 treated with Ro 08-2750 and 3 of Z138 treated with DMSO.

  Dataset EGAD00001009420

• Bulk RNA-Seq

  Human data for transcriptome (bulk RNA-Seq) in eight B-cell precursors: HSC, CLP, pro-B, pre-B, Immature B, Transitional B, Naive B CD5-, Naive B CD5+ cells

  Dataset EGAD00001010906

• Bulk ATAC-Seq Illumina NextSeq 500 (10M reads)

  Human data for chromatin accessibility (ATAC-Seq) in eight B-cell precursors: HSC, CLP, pro-B, pre-B, Immature B, Transitional B, Naive B CD5-, Naive B CD5+ cells

  Dataset EGAD00001010908

• Transcriptomic data in 46,XX, 46,XY, 47,XXY, 47,XYY individuals

  This dataset contains paired-end (151x2) RNA sequencing data (fastq files) from 25 human blood samples, some with sex chromosome aneuploidies. Data were generated using Illumina technology (Novaseq 6000) and a median of approximately 174 million pairs of reads per sample were obtained using two sequencing batchs. Samples come from: six 46,XX individuals, six 46,XY individuals, nine 47,XXY individuals, and four 47,XYY individuals.

  Dataset EGAD00001011202

• scRNA-seq

  This dataset gather scRNAseq data performed for MM.1S cell line in control and dex conditions at 4h and 24h

  Dataset EGAD00001011139

• Genome and transcriptome sequence data from a metastatic clear cell carcinoma of the ovary patient

  Genome and transcriptome sequence data from a metastatic clear cell carcinoma of the ovary patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001005906

• Genome-wide analysis for non alcoholic fatty liver disease

  Genome-wide association study for the 902 patients of non alcoholic fatty liver disease (NAFLD) including non alcoholic steato hepatitis (NASH) and hepatocellurar carcinoma and 7672 controls.

  Study JGAS000126

• BCG-Flu Challenge Study Human RNA-seq

  Whole blood RNA sequencing data generated from human samples collected as part of the BCG-Flu Challenge study. The dataset includes 746 samples. Paired-end sequencing was performed on an Illumina NovaSeq 6000 platform with a 150 bp paired-end configuration. Raw FASTQ files are provided.

  Dataset EGAD50000002407

• LUAD dataset

  This dataset includes 25 LUAD samples consisting of control samples derived from lymph node and tumor tissues samples, which were either untreated or treated with formalin and/or the NEBNext FFPE DNA Repair v2 Module. Sequencing was performed on the Illumina NovaSeq X platform using a 2×150 nt configuration, yielding approximately 18 Gbp per sample.

  Dataset EGAD50000001950

• 10x single-nucleus RNA-seq of postoperative human FCD II brain tissues

  This dataset contains 10x Genomics single-nucleus RNA sequencing data from postoperative brain tissues of patients with focal cortical dysplasia type II (FCD II). The samples were processed using the Chromium platform.

  Dataset EGAD50000001403

• Oxford Nanopore WGS

  A total of 20 individuals, were analyzed using Oxford Nanopore Technologies long-read sequencing. Each individual was sequenced on one PromethION flow-cell, providing approximately 25-30X coverage of the genome. The data is deposited as nanopore BAM files with methylation information included.

  Dataset EGAD50000000573

• Single-cell/single-nucleus RNA-seq of diffuse hemispheric gliomas, H3G34-mutant.

  9 DHG-H3G34 patient samples were sequenced by paired-end scRNA-sequencing using the Smart-Seq2 protocol on a NextSeq 500 sequencer (Illumina). Illumina bcl2fastq 1.5 was used for demultiplexing. This dataset contains the resulting 9,408 fastq files of 4,704 single cells/nuclei sequenced.

  Dataset EGAD50000000760

• RNA sequencing

  For RNA sequencing: All sample numbers starting with 6717 are tumor samples which has been sequenced using transcriptomics (see BAM files). It concerns biopsies of metastatic lesions from patients with BRAFV600 mutated melanoma, obtained before, during and after the study treatment (see samples metadata). RNA sequencing is performed using the Illumina Novaseq 6000 system.

  Dataset EGAD50000000383

• IBS-D RNA-seq raw data

  The data set consists of fastq raw files from RNA-seq of seven mucosal biopsies of the colon from seven patients, among them three patients with irritable bowel syndrome with diarrhea-predominant symptoms. Paired end sequencing on Illumina NovaSeq 6000 was used.

  Dataset EGAD50000000063

• NICOLA QUB Genetic

  Blood-derived DNA was obtained from samples within the NICOLA cohort. Genetic data was generated using the Illumina Infinium CoreExome-24 array (Illumina, USA) and is available for 2,978 participants (551,839 directly genotyped and 18,148,478 imputed single nucleotide polymorphisms following initial quality control). Genetic .bed .bim and .fam files are available.

  Dataset EGAD00010002762

• Combined genetic and transcriptome analysis of patients with Systemic Lupus Erythematosus (SLE)

  A comprehensive profiling of the genomic architecture of Systemic Lupus Erythematosus (SLE) by combining genetic and transscriptomic analysis by RNA-seq.

  Study EGAS00001003662

• 71 Whole-exome sequencing of Esophageal Squamous Cell Carcinoma on Chinese Patients

  Esophageal Squamous Cell Carcinoma (ESCC) is one of the deadliest cancers worldwide. We performed 71 Whole-exome sequencing of Esophageal Squamous Cell Carcinoma on Chinese Patients.

  Study EGAS00001001475

• 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

• Low coverage WGS from plasma DNA

  Low coverage whole genome sequencing plasma DNA from 50 male, 54 female non-cancer donors. For the analysis of nucleosomal positioning all data from the non-cancer controls were merged. Furthermore, two patients with metastasized breast cancer were sequenced on a NextSeq with higher depth.

  Dataset EGAD00001002215

• Chromatin 3D interactions mediate genetic effects on gene expression (RNA-seq)

  RNA-seq data for 168 Lymphoblastoid Cell Lines (LCL) and 78 Fibroblasts (FIB) from the Gencord Cohort. This dataset was generated as part of the following study: Delaneau et al (2019). Chromatin 3D interactions mediate genetic effects on gene expression.

  Dataset EGAD00001004872

• Wilms Tumour organoid sequencing WGS (2019-09-05)

  This study investigates the genomic and transcriptomic characteristics of Wilm's tumour organoids . This dataset contains all the data available for this study on 2019-09-05.

  Dataset EGAD00001005312

• RNAseq and genotypes from pancreatic islets (InsPIRE study).

  This is the data from the eQTLs InsPIRE study. This dataset includes RNAseq and genotypes from pancreatic islets and FAC sorted beta-cells, as well as RPKM values, covariates and cell count estimates.

  Dataset EGAD00001006149

• Whole exome sequencing analysis on patient-derived cervical cancer tissues and respective tumoroids

  Whole exome sequencing (WES) was performed on the matched tumor and organoid pairs from 7 cervical cancer patients. The DNA was sequenced on NovaSeq6000 platform with 8Gb sequencing coverage. WES data was mapped against human reference genome GRCh38 by using BWA (v0.7.5) mapping tool.

  Dataset EGAD00001006166

• Deep targeted re-sequencing of fetal tissues

  this data set includes deep targeted re-sequencing of fetal bulk tissues of the 4 foetuses (T21=2, D21=2). The tissues include: fetal skin and intestinal organoid cultures passage 0 of all 4 fetuses, and spleen of fetus N01 (T21)

  Dataset EGAD00001008474

• Correction of a Factor VIII genomic inversion with designer recombinases

  PromethION-based whole genome sequencing of endothelial cells differentiated from patient derived induced pluripotent stem cells (iPSCs) of a hemophilic donor, transiently treated with a Cre recombinase, a RecF8 recombinase, and untreated cells. The dataset contains fastq files with all sequencing reads passing the standard quality filtering.

  Dataset EGAD00001007923

• RNAseq of liver harvested from CDAHFD mice treated for 8 weeks with either the MGAT2 inhibitor compound BMS-963272 or vehicle

  This experiment consists of RNAseq of liver harvested from CDAHFD mice treated for 8 weeks with either the MGAT2 inhibitor compound BMS-963272 (N = 10) or with vehicle (N = 10).

  Dataset EGAD00001009389

• Combined single cell immunophenotyping and genotyping of adult low hypodiploid acute lymphoblastic leukemia

  This dataset includes the Fastq files from sequencing data generate from diagnostic and remission bone marrow mononuclear cell samples using the Mission Bio Tapestri Plateform with both DNA amplicons and protein from antibody-derived tags sequencing libraries.

  Dataset EGAD00001009763

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

  The dataset includes fastq files from 2 LCNEC tumors and matched PDTOs. The sequencing was done with either a Nextseq 2000 or a NovaSeq 6000 instrument.

  Dataset EGAD00001009993

• Linked-Read Medulloblastoma data

  Linked-read data from 25 medulloblastomas and their matching control. Dataset consists of 25 group 4 medulloblastomas (G4) as well as 2 sonic hedgehog medulloblastomas (SHH-MB) samples and 2 group 3 medulloblastomas. The data consists of BAM files generated by the LongRanger pipeline developed by 10x Genomics

  Dataset EGAD00001010849

• scRNA-seq dataset of A cycling, progenitor-like cell population at the root of atypical teratoid rhabdoid tumor subtype differentiation trajectories

  Study describing the differentiation trajectory...

  Dataset EGAD00001015545

• scATAC-seq dataset of A cycling, progenitor-like cell population at the root of atypical teratoid rhabdoid tumor subtype differentiation trajectories

  Study describing the differentiation trajectory...

  Dataset EGAD00001015546

• Whole-Genome Sequences from five human populations of Sudan

  This dataset provides the first high-coverage (~30X) whole-genome sequencing (WGS) data from Sudan, encompassing 125 individuals from five ethnolinguistic groups: Copts, Beja, Fulani, Fur, and Mahas. These populations represent three major linguistic families: Afro-Asiatic, Nilo-Saharan, and Niger-Congo, offering a detailed view of the country’s genetic diversity.

  Dataset EGAD00001015636

• Italian Primary Biliary Cirrhosis Study

  A Genome-wide association study of primary biliary cirrhosis (PBC) with an Italian cohort and loci meeting suggestive criteria were confirmed using a replication dataset from a previous Canadian study. The results confirmed associations for IL12A, IL12RB2, and HLA (peak between DQA1 and DQB1) and identified novel associations with IKZF3/ORMDL3 on chromosome 17, SPIB on chromosome 19, and IRF5 on chromosome. These studies also provided definition of haplotypic associations, differences between the PBC associated chromosome 17 haplotype and that of pediatric asthma and suggested several other genes as candidates for PBC susceptibility including DENND1B.

  Study phs000444

• Primary breast tumor heterogeneity through therapy

  We performed whole-exome sequencing on multiple regions (n=2-3) from four primary untreated breast tumors (n=1 HER2+, n=2 ER+/HER2-, n=1 triple-negative), as well as matched normal. We also performed whole-exome sequencing on one region from the pre-treatment diagnostic core biopsy and multiple regions (n=2-6) from the post-treatment surgical specimen for five HER2+ primary breast tumors, as well as matched normal; all were treated with combination chemotherapy and trastuzumab. Analysis of these specimens allows characterization of breast tumor heterogeneity and clonal evolution.

  Study EGAS00001003168

• Preferential infiltration of distinct Vγ9δ2 T cells into Glioblastoma multiforme

  Glioblastoma multiforme (GBM), the most fatal CNS cancer, is highly infiltrative as a result of phenotypic alteration of cancer cells mainly driven by a mutual interaction among cancer cells, tumor-associated macrophages (TAMs) and other stromal cells. This work aims at characterizing GBM-infiltrating γδ T cells that may regulate the GBM tumor microenvironment and cancer cell gene expression. V(D)J repertoires of tumor-infiltrating and blood circulating γδ T cells from 4 patients were analyzed by NGS-based TCR sequencing. RNA gene expression profiling and immunostaining of cancer tissues were performed as well.

  Study EGAS00001002790

• Integrative understanding of human immune system by functional genomics and development of intervention strategies for the prevention of autoimmune diseases

  arious peripheral blood immune cell subsets from 5 rheumatoid (RA) donors were collected ("CD16p_Mono", "CL_Mono???, "DN_B", "Fr_II_eTreg???, "mDC???, "Mem_CD4" , "Naive_B" , "Naive_CD4" , ???Neu", "NK" , "pDC" , "Plasmablast", ???SM_B", "Tfh", "Th1", "Th17", "Th2" , "USM_B"). The patients were analyzed again longitudinally after abatacept treatment. RNA-seq was performed with each immune cell subset samples. After gene expression quantification samples were filtered.

  Study JGAS000602

• 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

• THE GENOMIC LANDSCAPE OF ACTINIC KERATOSIS

  Dac EGAC00001001926

• Head of the Sequencing Unit

  Dac EGAC00001002698

• The AGGA Data Access Committee

  Dac EGAC00001003019

• Pooled Single-Cell RNA-Seq of iPSC-Derived Neural Stem Cells from ADHD and Control Individuals

  This dataset contains FASTQ files from pooled single-cell RNA sequencing (scRNA-seq) of neural stem cells (NSCs) derived from induced pluripotent stem cells (iPSCs). The iPSCs were reprogrammed using the non-integrative Sendai virus system (CytoTune-iPS 2.0), introducing OCT3/4, SOX2, KLF4, and cMYC. Donor somatic cells included keratinocytes, PBMCs, and lymphoblastoid cell lines from individuals with ADHD and age-matched healthy controls (6–18 years). iPSCs underwent standard quality control, including immunocytochemistry, qRT-PCR, mycoplasma testing, and SNP genotyping. NSCs were produced via neural induction and validated by qRT-PCR and immunostaining for PAX6, SOX2, NESTIN, TUJ1, and FOXG1. Sequencing was performed on the Illumina NovaSeq 6000.

  Dataset EGAD00001015644

• WGS of clonal organoids, bulk-tumor tissues, and matched blood samples derived from metastatic colorectal cancer patients

  This dataset consists of WGS fastq files from 58 clonal organoids and 18 fresh-frozen (FT) bulk-tissue samples from surgically resected primary and metastatic tumors before and after anticancer therapies in 6 patients with matched blood control samples from each patient. After DNA extraction from each sample using DNeasy Blood and Tissue Kit (Qiagen), library preparation was done using TruSeq DNA PCR-free kit. Then, paired-end fastq files were generated using Illumina NovaSeq 6000.

  Dataset EGAD50000001493

• APS-1 Immune Panel Sequencing

  Single cell sequencing of expanded regulatory T cells (Tregs) in 8 APS-1 patients and 8 age and gender matched controls (same patients and controls as for global gene expression and TCR sequencing, excluding one for each group (control sample and patient sample #13)). Each Sample has two technical repeats. 10x Genomics Target Hybridization Kit and Human Immunology Panel was used with GEX libraries.

  Dataset EGAD50000000262