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• Autozygosity pilot - British-Pakistani from Birmingham 2

  The offspring of first cousin marriages have ~6% of their genome autozygous, i.e. homozygous identical by descent, or even more if there was further consanguinity in their ancestry. In the UK there are large populations with very high first cousin marriage rates of 20-50%. Sequencing the exomes of a sample of these individuals has the potential both to support genetic health programmes in these populations, and to provide genetic research information about rare loss of function mutations. This pilot study based on existing British-Pakistani cohort samples from Birmingham will identify homozygous individuals for almost all variants down to an allele frequency around 1%, plus individuals carrying hundreds of new homozygous rare loss-of-function variants, and will support development of community relations and ethics for a wider study currently being designed. The data deposited in the EGA consists of low coverage whole exome sequencing on these samples.

  Dataset EGAD00001001026

• Autozygosity pilot - British-Pakistani from Birmingham

  The offspring of first cousin marriages have ~6% of their genome autozygous, i.e. homozygous identical by descent, or even more if there was further consanguinity in their ancestry. In the UK there are large populations with very high first cousin marriage rates of 50-80%. Sequencing the exomes of a sample of these individuals has the potential both to support genetic health programmes in these populations, and to provide genetic research information about rare loss of function mutations. This pilot study based on existing British-Pakistani cohort samples from Birmingham will identify homozygous individuals for almost all variants down to an allele frequency around 1%, plus individuals carrying hundreds of new homozygous rare loss-of-function variants, and will support development of community relations and ethics for a wider study currently being designed. The data deposited in the EGA consist of low coverage whole exome sequencing on these samples.

  Dataset EGAD00001001025

• Targeted bisulfite sequencing

  Raw reads from targeted bisulfite sequencing. The SureSelect Methyl-Seq target enrichment system (Agilent Technologies, Inc., CA, USA) was used to prepare bisulfite sequencing libraries from blood DNA samples of lymphoma patients (Ly1, Ly2), healthy family members (Ly8, Ly9, Ly10, Ly11, Ly12, Ly13 and Ly14), baseline controls (Control1-5), DNMT3A mutation carriers (Id5, Id7, Id9, Id11) and their age-matched controls (Id6, Id8, Id10, Id12). In addition, blood DNA sample of a patient (HLRCC_N7) with germline fumarate hydratase (FH) mutation is included. Illumina paired-end sequencing for targeted libraries from Ly1, Ly2, Ly8, Ly9, Ly10 and Ly11 was done at Karolinska Institutet using 100 base-pair read length and the HiSeq2000 platform. Illumina paired-end sequencing for targeted libraries from Ly12, Ly13, Ly14, and DNMT3A mutation carriers and their age-matched controls was done as a service at BGI (BGI Tech Solutions Co., Ltd., China) using 126 base-pair read length and the HiSeq2500 platform.

  Dataset EGAD00001004785

• scDNA-seq for 'Early evolutionary branching across spatial domains predisposes to clonal replacement under chemotherapy in neuroblastoma'

  Neuroblastoma (NB) is one of the most lethal childhood cancers due its propensity to treatment resistance. By spatial mapping of subclone geographies before and after chemotherapy across 89 tumor regions from 12 NBs, we find that densely packed territories of closely related subclones present at diagnosis are replaced under effective treatment by islands of distantly related survivor subclones, originating from a different most recent ancestor compared to lineages dominating before treatment. Conversely, in tumors that progressed under treatment, ancestors of subclones dominating later in disease are present already at diagnosis. Chemotherapy treated xenografts and cell culture models replicates these two contrasting scenarios and shows branching evolution to be a constant feature of proliferating NB cells. Phylogenies based on whole genome sequencing of 505 individual NB cells indicate that a rich repertoire of parallel subclones, emerges already with the first oncogenic mutations and lays the foundation for clonal replacement under treatment.

  Dataset EGAD00001015414

• RNA-sequencing of meningiomas for integrative molecular classification.

  RNA-sequencing of meningiomas for integrative molecular classification.

  Dataset EGAD00001007494

• EGAD00010000702

  SNP-chip genotyping data for one proband in the DDD study (Ref : Carvalho AJHG 2015)

  Dataset EGAD00010000702

• Tetralogy of Fallot Exome Trios

  Exome sequencing of 30 parent-offspring trios to >50X mean depth, where the offspring has sporadic TOF, to identify potential causal de novo mutations. We will use the exome plus design for pulldown that incorporates ~6.8Mb of additional regulatory sequences in addition to the ~50Mb GENCODE exome.

  Dataset EGAD00001000344

• Pakistan_Damgaard2018

  Genotype data for 140 present-day individuals from five populations in Pakistan in The first horse herders and the impact of early Bronze Age steppe expansions into Asia DOI: 10.1126/science.aar7711. Sampling details are presented in supplementary section S2.1 Data generation

  Dataset EGAD00010001678

• Genotype data for 4607 Greenlandic samples (MEGA array)

  This file fileset has 4607 Greenlanders scored on the Illumina MEGA array (1,622,813 sites), and has been put on the plus strand. The data is in PLINK bed/bim/fam format. The Greenlandic individuals originate from two population surveys, B99 and IHIT.

  Dataset EGAD00010002057

• Genotyping_data_total

  Genotyping data for ACE2 (rs2285666), MX1 (rs469390) and TMPRSS2 (rs2070788) variants. Patients are classified as mild (n=34) and severe (n=32). DNA genotyping was performed using the TaqMan® Genotyping Master Mix (Applied Biosystems). Allelic discrimination assays were performed on a 7900HT Fast Real-Time PCR System (Applied Biosystems).

  Dataset EGAD00010002445

• ImmuNEO CD8 cell lines

  Paired RNA-Seq data from 16 samples of different tumors CD8+ T cells added to the study "Proteogenomic analysis reveals RNA as a source for tumor-agnostic neoantigen identification (H021)". Sequencing was performed on Illumina NextSeq 500. The sequencing was always paired

  Dataset EGAD50000000193

• AmsterdamUMC Data Access Committee for the study "Multi-omic analysis of thyroid dysfunction in Down Syndrome"

  The current data access committee reviews and assesses data requests of researchers that seek to gain access to data acquired as part of the "Multi-omic analysis of thyroid dysfunction in Down Syndrome" study as performed at the AmsterdamUMC, Amsterdam, Netherlands.

  Dac EGAC50000000186

• RNA_TPO3_2023

  Human engineered CRC organoids (APC KO; KRAS G12D; TP53 KO) were grown in either glucose or lactate, in the presence and absence of DCA or BRD4 inhibition (JQ1). Samples were collected and processed for bulk RNA-seq.

  Dataset EGAD50000000089

• BAM files from whole-genome sequencing of 3 agressive B-cell lymphoma tumour and non-tumor samples

  This dataset contains BAM files from whole-genome sequencing (WGS) of 3 agressive B-cell lymphoma tumour samples for cases 1, 6, and 7 as well as the corresponding non-tumor whole-genome sequencing BAM files.

  Dataset EGAD50000000800

• CAIRO2 - Whole Exome Sequencing (WES)

  Long-term Survival Update and Extended RAS Mutational Analysis of the CAIRO2 Trial: Addition of Cetuximab to CAPOX/Bevacizumab in Metastatic Colorectal Cancer. Whole Exome Sequencing (WES) of 64 metastatic colorectal cancer (mCRC) from CAIRO2 trial. WES data was used for mutational analysis.

  Dataset EGAD50000001140

• CAIRO2 - Shallow Whole Genome Sequencing (sWGS)

  Long-term Survival Update and Extended RAS Mutational Analysis of the CAIRO2 Trial: Addition of Cetuximab to CAPOX/Bevacizumab in Metastatic Colorectal Cancer. Shallow Whole Genome Sequencing (sWGS) of 52 metastatic colorectal cancer (mCRC) samples from CAIRO2 trial. sWGS was used for mutational analysis.

  Dataset EGAD50000001141

• Single-cell sequencing of PBMC & CSF in neuroinflammatory disorders

  Single-cell sequencing and genotyping for Cambridge samples analyzed as part of a project evaluating single-cell gene expression & lymphocyte receptor sequences in CSF and PBMC of MS and other neuroinflammatory disorders.

  Dataset EGAD50000001023

• Patient-derived xenograft models of head and neck cancers

  Establishment and characterization of two patient-derived xenograft models from HNSCC patients , initiatlly treatment-naive, and for which cetuximab-acquired resistant model couterparts have been generated. All models have been characterized at genomic level. HNSCC tissues were obtained from surgical resections at Cliniques universitaires St Luc in Brussels (Belgium).

  Dac EGAC50000000502

• MethylBERT enables read-level DNA methylation pattern identification and tumour deconvolution using a Transformer-based model

  This is the DAC for the study "MethylBERT enables read-level DNA methylation pattern identification and tumour deconvolution using a Transformer-based model" of Pavlo Lutsik (DKFZ B370/KU Leuven, pavlo.lutsik@kuleuven.be) and Clarissa Gerhauser (DKFZ B370, c.gernauser@dkfz.de)

  Dac EGAC50000000497

• Whole Exome Sequencing (WES) data of PERFECT trial

  Whole exome sequencing (WES) data of patients with resectable esophageal adenocarcinoma treated with neoadjuvant atezolizumab and chemoradiation (PERFECT). 78 matched samples (Tumor-Normal) from 39 patients with resectable esophageal adenocarcinoma of the PERFECT trial. Whole exome sequencing performed for mutation detection analysis.

  Dataset EGAD50000001153

• NICHE - RNA-seq of MMR proficient early stage colon cancers

  The dataset includes 29 FASTQ files from single-end total RNA sequencing on Illumina HiSeq2500 and 66 files from 33 paired-end RNA sequencing samples on Novaseq 6000 for 31 pMMR colon cancer patients.

  Dataset EGAD50000001248

• RNA-Seq dataset for malignant pleural and peritoneal mesothelioma

  This dataset contains RNA sequencing data of pleural and peritoneal mesothelioma. The number of samples is 18. Sequencing was performed on Illumina NovaSeq 6000 and Illumina NovaSeqXPlus. The sequencing was always paired.

  Dataset EGAD50000001342

• Small RNA sequencing of human oocytes and early embryos

  This dataset contains single-end fastq files for human oocytes (n=12), zygotes (n=5), and early embryos (n=10) sequenced with Illumina NextSeq500. The sequencing libraries were prepared from single oocytes, zygotes, and embryos in two batches.

  Dataset EGAD50000000227

• Targeted next-generation sequencing of plasma samples

  Targeted next-generation sequencing was performed on circulating cell-free DNA extracted from plasma samples of patients in the Neo-Pembro trial. For each patient, circulating cell-free DNA from the baseline plasma sample was extracted and sequenced using the AVENIO Expanded Kit v2.

  Dataset EGAD50000001415

• Targeted capture sequencing from High-grade B-cell lymphoma, not otherwise specified: an LLMPP study

  Targeted capture sequencing for 366 newly added samples in High-grade B-cell lymphoma, not otherwise specified: an LLMPP study and 29 samples from a previously uploaded dataset.

  Dataset EGAD50000001364

• Extracellular Vesicle miRNA Sequencing with Qiaseq and NextSeq 550

  This dataset includes small RNA sequencing data from extracellular vesicle-derived RNA. miRNA libraries were prepared using the Qiaseq miRNA Library Kit with adaptations for low RNA input and sequenced on the Illumina NextSeq 550 platform

  Dataset EGAD50000001504

• RNA-Seq of primary pediatric kidney tumor controls for the soft tissue sarcoma tumoroid biobank

  Dataset EGAD00001008709

• Dac for "ARHGAP11A Maintains Cortical Progenitor Identity Through RHOA–ROCK Signalling During Human Brain Development" with Julia.ladewig@zi-mannheim.de, Department of Translational Brain Research. Moritz Mall, m.mall@dkfz-heidelberg.de, German Cancer Research Center (DKFZ). Yannick Hass, yannick.hass@zi-mannheim.de, Department of Translational Brain Research. Anne Hoffrichter, anne.hoffrichter@zi-mannheim.de, Department of Translational Brain Research, Central Institute of Mental Health

  Dac EGAC00001003603

• cfDNA sWGS BAM — Metastatic colorectal cancer

  Plasma cirDNA sWGS for metastatic colorectal adenocarcinoma at diagnosis prior to systemic therapy. Libraries DSP/SSP (per sample). Sequencing by IntegraGen (2022–2024). Alignment: GRCh38 with BWA-MEM; BAMs sorted/indexed; delivered as primary mapped reads only (filters/MAPQ in analysis metadata). Controlled access

  Dataset EGAD50000001879

• Ultra-long whole-genome and Cas9-targeted nanopore sequencing of fibroblasts: FSHD, BAMS, healthy controls

  Data from the D4Z4End2End study (Xiao et al. 2025), for genetic and epigenetic analysis of the D4Z4 macrosatellite in health and disease.

  Dataset EGAD50000001551

• HOVON152 Trial shallow Whole Genome Sequencing

  Associated with Molecular profiling of HGBCL-DH-BCL2 patients treated in the HOVON-152 triaL. Targeted sequencing of 30 samples from 30 High-grade B-cell lymphoma patients. Targeted sequencing was used for identify genomic alterations associated with patient outcome.

  Dataset EGAD50000002094

• Single-cell RNA-sequencing for peripheral blood mononuclear cells from COVID-19 patients and healthy controls of Japanese

  We performed single-cell RNA-sequencing of peripheral blood mononuclear cells obtained from COVID-19 patients and healthy controls.

  Study JGAS000593

• Single-cell RNA-sequencing for peripheral blood mononuclear cells from COVID-19 patients and healthy controls of Japanese

  We performed single-cell RNA-sequencing of peripheral blood mononuclear cells obtained from COVID-19 patients and healthy controls.

  Study JGAS000543

• Searching for DNA methylation sites associated with panic disorder

  This study aimed to identify whole-genome DNA methylation profile of panic disoeder and to search DNA methylation sites associated with the disease

  Study JGAS000111

• Dataset for desmoplastic small round cell tumor - WGS

  This dataset contains 25 WGS sequencing samples of patients with desmoplastic small round cell tumor. Sequencing was performed on Illumina HiSeq X and NovaSeq 6000 using Illumina TruSeq Nano DNA Kit. The sequencing was always paired.

  Dataset EGAD50000000911

• WGS for 21 samples

  This dataset contains whole-genome sequencing (WGS) data from 14 acute leukemia cases of the newly identified FOXF1/FENDRR ALL subtype, including diagnosis or relapse samples, as well as 7 matched germline samples. All the 21 samples are in bam file type.

  Dataset EGAD50000001790

• Sorted WGS for three samples

  This dataset contains Whole Genome Sequencing (WGS) data from two cell populations (myeloid and lymphoid) and the germline population sorted from a primary sample of the novel FOXF1/FENDRR ALL subtype. All the three samples are in bam file type.

  Dataset EGAD50000001792

• WES dataset

  Associated with Molecular biomarkers in progression from refractory celiac disease to the lethal cancer variety enteropathy associated T cell lymphoma (EATL) Study. Whole Exome Sequencing (WES) of 63 samples. WES analysis done to detect mutations and copy number aberration predictive for progression from RCD to EATL.

  Dataset EGAD50000001164

• Exome sequencing data for 40 cases of alopecia areata and vitiligo

  Sequencing of independent unrelated cases of alopecia areata (total/ universal) and vitiligo (>10%, affected family member). DNA obtained from blood

  Study EGAS00001003831

• SF12017 snATAC Seq IDH1 Mutant GBM 55, Male

  IDH1 mutant GBM 55, Male. Single Nuclei ATAC seq data from high grade human glioma samples. NovaSeq6000 was used for ATAC seq. The files uploaded are bam files created with grch38 reference.

  Dataset EGAD00001005405

• SF11612 snATAC Seq Recurrent oligodendroglioma

  SF11612 Recurrent oligodendroglioma. Gender Male Age 67. Single Nuclei ATAC seq data from low grade human glioma samples. NovaSeq6000 was used for ATAC seq. The files uploaded are bam files created with grch38 reference.

  Dataset EGAD00001005413

• DKFZ-St.Jude Medulloblastoma - 70 PAN-GATC control exomes

  Exome controls for 70 individuals, PAN-GATC cohort, sequenced on Illumina machines from the paper "Germline Elongator mutations in Sonic Hedgehog medulloblastoma" (Waszak et al. 2020 Nature).

  Dataset EGAD00001006661

• Blood plasma and paired genomic DNA from neuroblastoma patients

  The dataset is comprised of 3 blood plasma samples (Patient 1-3_plasma_cfDNA) paired with genomic DNA (Patient 1-3_tumor gDNA) from the corresponding primary neuroblastoma from three patients. For all these samples whole-exome sequencing (WES) data have been generated.

  Dataset EGAD00001006012

• Leiomyosarcoma RNA-Seq

  RNA was extracted from fresh frozen LMS material for 29 untreated tumors (24 primary tumors, 5 metastatic12 relapses) and 13 tumors treated with radiation(7 primaries, 6 metastatic relapses). RNA-Seq sequencing was performed using established protocols on Illumina HiSeq 2500

  Dataset EGAD00001006628

• SMRT-seq

  In this study, we enhanced 5mC detection using SMRT sequencing by holistically analyzing kinetic signals of a DNA polymerase and sequence context for every base within a measurement window. We employed a convolutional neural network to train a methylation classification model.

  Dataset EGAD00001006875

• CASCADE Metastatic Melanoma Rapid Autopsy sequencing data

  Sequence data (paired-end FASTQ format) for 209 samples from 73 sample sites, from 7 individuals. Samples include primary melanomas, metastatic tumours and ctDNA

  Dataset EGAD00001006867

• Subset of EGAS00001004662 WGS data (2 tumor/control pairs) which are used in EGAS00001004813 (Titel: Comprehensive Genomic and Transcriptomic Analysis of Rare Cancers for Guiding of Therapy (H021))

  Part of the published data from EGAS00001004662 resulted in the publication of this study EGAS00001004813

  Dataset EGAD00001008906

• Sequencing data for oesophageal / related samples - Foley, Shorthouse et al (RNA)

  Data supporting: "SMAD4 and KCNQ3 Alterations are Associated with Lymph Node Metastases in Oesophageal Adenocarcinoma" RNAseq (FASTQ files) 6 samples

  Dataset EGAD00001011065

• HV31 - Bionano DLS optical mapping

  Bionano DLS optical mapping data for individual HV31 generated using DNA from peripheral blood mononuclear cells, to a molecule depth of ~153×. Optical mapping was performed at the Weatherall Institute of Molecular Medicine using the Bionano Saphyr platform.

  Dataset EGAD00001007049

• Transcription factor binding in human monocyte differentiation

  This dataset consists of ChIP-seq data data from human monocytes, monocyte-derived dendritic cells as well as monocyte-derived cells that were subjected to mRNA transfection for PU.1, IRF4, and EGR2. In total, it the data set includes 18 samples.

  Dataset EGAD00001006602

• Ampliseq library database

  This database contains 46 samples for early stage ovarian high grade serous carcinoma project. Amplicon sequencing on 37 tumour samples from early stage ovarian high grade serous carcinoma as well as 5 adjacent normal tissue samples and 4 whole blood samples.

  Dataset EGAD00001008587

• Immune single-cell profiling of human chronic inflammatory skin disease

  This dataset includes 10X Genomics 3' single cell-RNA-seq profiles from 24 human rashes and 7 healthy controls. BAM files are provided for each sample.

  Dataset EGAD00001008624

• PSC-IBD-CRC

  Formalin-fixed, paraffin-embedded samples from 19 PSC-IBD-CRCs, 15 adjacent (non-tumour) mucosa samples and 18 non-mucosal DNA samples were collected via the nationwide network and registry of histo- and cytopathology in the Netherlands (PALGA). DNA was extracted for molecular analysis.

  Dataset EGAD00001006226

• SF12264 snRNA-Seq Primary GBM

  Single Nuclei RNA-Seq Primary GBM. Gender Female Age 51. Single Nuclei RNA seq from high grade primary glioma sample. NovaSeq6000 was used for RNA seq. The files uploaded are bam files created with grch38 reference.

  Dataset EGAD00001005410

• EFFORT occupationally exposed human stool metagenomes (148 samples)

  Metagenomes of stool samples from 54 pig farmers, 24 broiler farmers and 70 slaughter line workers. Note: Access to the data will only be granted for antibiotic resistance studies in accordance with the EFFORT consents issued by the participants.

  Dataset EGAD00001005444

• PacBio HiFi sequencing of telobait-captured DNA from 48 patients

  PacBio HiFi sequencing was performed on 48 barcoded patients' genomic DNA after a telobait-capture protocol to enrich for telomeric regions. The sequencing reads of each patient were de-multiplexed and presented as patient-specific PacBio CCS BAM files.

  Dataset EGAD00001008626

• Data for noninvasive lung cancer subtyping study

  This dataset included cfMethyl-Seq data of 15 plasma cfDNA samples from 15 lung cancer patients and RRBS data of 58 lung tumor tissue samples from 58 lung cancer patients. The data were generated following the standard protocols.

  Dataset EGAD00001015344

• Dataset for Ewing_sarcoma_PNET-WHOLE_GENOME

  Rare cancer sequencing data of 18 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008874

• ICGC PCAWG Dataset: LINC-JP_PCAWG_WGS_BWA

  ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: LINC-JP.

  Dataset EGAD00001002662

• Fecal 16S HV sequencing data

  Fecal 16S-V4 rRNA gene sequence data from NCT02749630 healthy volunteers. Stool samples were collected at screening as well as on days 29, 43, 64, 85, and 134 processed for 16SV4 rRNA gene sequencing

  Dataset EGAD00001008840

• Dataset for colorectal_cancer-WHOLE_GENOME

  Rare cancer sequencing data of 54 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008872

• CBD-RAW-SC-ATAC: 10X Single-Cell ATAC

  Raw Illumina sequencing data from single-cell ATACSeq experiments. For further information regarding this dataset, please contact Julian Knight and Tatjana Sauka-Spengler at contact@combat.ox.ac.uk.

  Dataset EGAD00001007963

• SF11331 snATAC Seq Primary GBM Male

  SF11331 Primary GBM Male,55 Single Nuclei ATAC seq data from high grade human glioma sample. NovaSeq6000 was used for ATAC seq. The files uploaded are bam files created with grch38 reference.

  Dataset EGAD00001005408

• SF11949 snATAC Seq IDH1 mutant oligodendroglioma Male

  IDH1 mutant oligodendroglioma male, 40. Single Nuclei ATAC seq data from low grade human glioma sample. NovaSeq6000 was used for ATAC seq. The files uploaded are bam files created with grch38 reference.

  Dataset EGAD00001005398

• WGS

  Whole Genome sequencing. 1 ug of genomic DNA from each lymph node sample was used for the construction of a TruSeq DNA PCR Free (350) library before sequencing in a Illumina HiSeq X Ten (2 × 151 bp). Mean coverage 30x.

  Dataset EGAD00001005423

• Data set for pan.met study

  The dataset referenced by EGA Study ID EGAS00001004208 includes 20 human exome sequencing data and 11 human RNA sequencing data from tumor or normal tissues. Each sequencing data includes two pair-end short read files in fastq format.

  Dataset EGAD00001005957

• Dataset for LCPlus_WES

  WES/WGS sequencing data of 86 chromothriptic tumor and control runs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001009273

• Single cell RNA sequencing of tumor and ascites in high grade ovarian cancer

  Fastq files for single cell RNA sequencing of cells from ovarian cancer tumor and ascites (10X chromium 5' v1.1 libraries). Multiple cases are pooled in each sequencing library.

  Dataset EGAD00001006627

• CBD-RAW-RNASEQ: Bulk RNAseq data

  Bulk RNAseq data from whole blood. For further information regarding this dataset, please contact Katie Burnham and Andew Kwok at contact@combat.ox.ac.uk.

  Dataset EGAD00001007957

• CBD-RAW-SC-VDJ-B: 10X Single-Cell VDJ BCR

  Raw Illumina sequencing data. For further information regarding this dataset, please contact Rachael Bashford-Rogers at contact@combat.ox.ac.uk.

  Dataset EGAD00001007964

• HV31 - De novo assembly of eight immune system regions

  De novo assembly of eight immune system regions for individual HV31, generated using a multi-platform pipeline. A full description of the generation of these assemblies can be found at https://doi.org/10.1101/2021.02.03.429586.

  Dataset EGAD00001007050

• SF11215 snATAC Seq GBM

  High grade glioma sample, Gender Male Age 46. Single Nuclei ATAC seq data from high grade human glioma samples. NovaSeq6000 was used for ATAC seq. The files uploaded are bam files created with grch38 reference.

  Dataset EGAD00001005407

• In Utero MPN Twin WGS Data

  The dataset contains sequencing data generated for the publication 'In utero origin of myelofibrosis presenting in adult monozygotic twins after a prolonged disease latency.

  Dataset EGAD00001008319

• 17 scRNAseq samples

  17 samples were processed for single cell RNA sequencing (SORT-seq)

  Dataset EGAD00001007523

• scRNA-seq dataset for AD and Pso patients

  This dataset contains scRNA-seq fastq files to the paper entitled "Single-cell profiles reveal distinctive immune response in atopic dermatitis in contrast to psoriasis". The details of experiment setup was described in the paper.

  Dataset EGAD00001010106

• Transcriptome Analysis of CLL patient samples

  This dataset includes Illumina RNA Sequencing Data for 59 chronic lymphocytic leukemia patient samples. 57 samples are single end, 2 samples are paired end sequencing.

  Dataset EGAD00001008320

• WGS data subfolder for normal tissue from multifocal ileal NETs study

  This dataset includes linked-read whole-genome sequencing data from the normal ileal of the patient. The normal sample was sequenced using the 10x Genomics linked-read whole-genome sequencing (WGS) approach.

  Dataset EGAD00001008491

• cell-free methylated DNA immunoprecipitation and high-throughput sequencing data for samples from liver transplant recpients with graft pathologies

  Bam and indexed bam files after removal of duplicates and trimming of the unique molecular identifiers. Sequencing was performed on NovaSeq 6000 platform.

  Dataset EGAD00001010305

• Dataset for NSCLC-EXON

  Rare cancer sequencing data of 42 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008892

• Long-read sequencing for cell-free DNA analysis (human)

  31 pregnant women at different trimesters, 6 hepatitis B carriers, and 8 patients with hepatocellular carcinoma

  Dataset EGAD00001008980

• CITE-Seq (Cellular Indexing of Transcriptomes and Epitopes by Sequencing) of CLL_24

  To explore intratumor-heterogeneity of CLL_24 using single-cell multi-omics approach, we generated single-cell CITE-seq data for CLL_24, coupling scRNA-seq and protein surface marker measurements with oligo-tagged antibodies.

  Dataset EGAD00001009174

• Gene panel sequencing of B precusor acute lymphoblastic leukemia

  Targeted gene panel sequencing for 206 genes with relevance in normal an leukemic lymphopoiesis was performed in bone marrow / peripheral blood samples from n=96 patients with first diagnosis of B cell precursor acute lymphoblastic leukemia.

  Dataset EGAD00001010070

• Kidney tumour_DNA (2018-09-19)

  This is a bulk DNA and RNA sequencing study of human renal tumours . This dataset contains all the data available for this study on 2018-09-19.

  Dataset EGAD00001004346

• ESGI - Whole Genome Sequencing of samples from the Croatian isolated populations (2017-11-22)

  Whole genome sequencing of sampels from isolated populations from Croatia. The samples are sequenced using the Illumina HiSeq X Ten system. This dataset contains all the data available for this study on 2017-11-22.

  Dataset EGAD00001003812

• ICGC PCAWG Dataset: PAEN-AU_PCAWG_WGS_BWA

  ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: PAEN-AU.

  Dataset EGAD00001002154

• ICGC PCAWG Dataset: LICA-FR_PCAWG_WGS_BWA

  ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: LICA-FR.

  Dataset EGAD00001002016

• RNA-seq colorectal adenomas NKI-AvL TGO series NGS-ProToCol

  The dataset "RNA-seq colorectal adenomas NKI-AvL TGO series NGS-ProToCol" includes 2 x 30 fastq files from paired-end total RNA sequencing on Illumina HiSeq2500 for 30 snap-frozen colorectal adenomas.

  Dataset EGAD00001004055

• Low-coverage Whole Genome Sequencing, colorectal adenomas NKI-AvL TGO series NGS-ProToCol

  The dataset "Low-coverage Whole Genome Sequencing, colorectal adenomas NKI-AvL TGO series NGS-ProToCol" includes 30 fastq files from single-end low-coverage WGS on Illumina HiSeq2500 for 30 snap-frozen colorectal adenomas.

  Dataset EGAD00001004092

• CNA vcf files for CPCG Subclonal Heterogeneity in multiple and single regions

  CNA calls generated using the SomaticSniper-TITAN-PhyloWGS from the CPC-GENE Subclonal Heterogeneity study using single and multiple regions

  Dataset EGAD00001004440

• ICGC PCAWG Dataset: PACA-CA_PCAWG_WGS_BWA

  ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: PACA-CA.

  Dataset EGAD00001003162

• ICGC PCAWG Dataset: CLLE-ES_PCAWG_RNA-Seq_TopHat2

  ICGC PCAWG Dataset for RNA-Seq BAM aligned using TopHat2. Project: CLLE-ES.

  Dataset EGAD00001003548

• ICGC PCAWG Dataset: LIRI-JP_PCAWG_RNA-Seq_Star

  ICGC PCAWG Dataset for RNA-Seq BAM aligned using Star. Project: LIRI-JP.

  Dataset EGAD00001003547

• ICGC PCAWG Dataset: CLLE-ES_PCAWG_RNA-Seq_Star

  ICGC PCAWG Dataset for RNA-Seq BAM aligned using Star. Project: CLLE-ES.

  Dataset EGAD00001003549

• ICGC PCAWG Dataset: RECA-EU_PCAWG_RNA-Seq_TopHat2

  ICGC PCAWG Dataset for RNA-Seq BAM aligned using TopHat2. Project: RECA-EU.

  Dataset EGAD00001003559

• ICGC PCAWG Dataset: MALY-DE_PCAWG_WGS_BWA

  ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: MALY-DE.

  Dataset EGAD00001002123

• ICGC PCAWG Dataset: BOCA-UK_PCAWG_WGS_BWA

  ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: BOCA-UK.

  Dataset EGAD00001002125

• CLL targeted exome sequencing (2018-03-14)

  Aim to characterise cancer gene landscape in CLL, particularly in cases with mutated POT1 gene. Treatment-naive CLL cases will be interrogated by targeted exome sequencing using a cancer gene panel. . This dataset contains all the data available for this study on 2018-03-14.

  Dataset EGAD00001004037

• ICGC PCAWG Dataset: PACA-AU_PCAWG_RNA-Seq_TopHat2

  ICGC PCAWG Dataset for RNA-Seq BAM aligned using TopHat2. Project: PACA-AU.

  Dataset EGAD00001003411

• ICGC PCAWG Dataset: PACA-AU_PCAWG_RNA-Seq_Star

  ICGC PCAWG Dataset for RNA-Seq BAM aligned using Star. Project: PACA-AU.

  Dataset EGAD00001003410

• ICGC PCAWG Dataset: MALY-DE_PCAWG_RNA-Seq_Star

  ICGC PCAWG Dataset for RNA-Seq BAM aligned using Star. Project: MALY-DE.

  Dataset EGAD00001003560