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• ICGC PCAWG Dataset: RECA-EU_PCAWG_WGS_BWA

  ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: RECA-EU.

  Dataset EGAD00001002131

• ICGC PCAWG Dataset: EOPC-DE_PCAWG_WGS_BWA

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

  Dataset EGAD00001002124

• 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

• ICGC PCAWG Dataset: BRCA-EU_PCAWG_WGS_BWA

  ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: BRCA-EU.

  Dataset EGAD00001002129

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

  The dataset "RNA-seq colorectal carcinomas 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 carcinomas.

  Dataset EGAD00001004056

• 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

• CancerSEEK ctDNA FASTQ files

  Sequencing data from 1,005 cancer patients and 812 healthy controls. All samples prepared using Safe-SeqS technology and sequenced on an Illumina MiSeq and/or HiSeq instrument. Paired FASTQ files for correspond to read 1 and the index read present (R and I respectively).

  Dataset EGAD00001003931

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

  SNV calls generated using the MuTect-Battenberg-PhyloWGS from the CPC-GENE Subclonal Heterogeneity study using single and multiple regions

  Dataset EGAD00001004434

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

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

  Dataset EGAD00001004432

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

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

  Dataset EGAD00001004442

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

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

  Dataset EGAD00001004443

• 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

• ICGC PCAWG Dataset: PRAD-UK_PCAWG_WGS_BWA

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

  Dataset EGAD00001002126

• Epigentic sequence data of monocytes and macrophages

  Data for paper: Epigenetic dynamics of monocyte to macrophage differentiation with Chip Seq, NOMe, mRNA, total RNA, noncoding RNA, whole genome bisulfite seq,

  Dataset EGAD00001002201

• 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

• BLUEPRINT September 2016, ATAC-seq Chronic Lymphocytic Leukemia from venous blood, on Genome GRCh38

  ATAC-seq data for 106 sample(s) Chronic Lymphocytic Leukemia from venous blood, on Genome GRCh38. 111 run(s), 109 experiment(s), 109 alignment(s). Part of BLUEPRINT (September 2016).

  Dataset EGAD00001002916

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

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

  Dataset EGAD00001004431

• 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

• 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

• 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

• ICGC PCAWG Dataset: PACA-AU_PCAWG_WGS_BWA

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

  Dataset EGAD00001002132

• 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

• 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

• 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 EGAD00001004441

• 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

• ICGC PCAWG Dataset: RECA-EU_PCAWG_RNA-Seq_Star

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

  Dataset EGAD00001003558

• 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

• Whole Transcriptome Sequencing

  RNA-seq data of 15 snap-frozen tissue of peritoneal mesothelioma. The strand specific RNA library prepared using TruSeq (Illumina) and pair-end sequencing performed in Illumina HiSeq 4000. The datasets contains paired fastq files for each of 15 tumor samples.

  Dataset EGAD00001004504

• ICGC PCAWG Dataset: ESAD-UK_PCAWG_WGS_BWA

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

  Dataset EGAD00001002156

• ICGC PCAWG Dataset: MELA-AU_PCAWG_WGS_BWA

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

  Dataset EGAD00001002157

• ICGC PCAWG Dataset: LIRI-JP_PCAWG_WGS_BWA

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

  Dataset EGAD00001002155

• BLUEPRINT September 2016, ATAC-seq Mantle Cell Lymphoma from venous blood, on Genome GRCh38

  ATAC-seq data for 5 sample(s) Mantle Cell Lymphoma from venous blood, on Genome GRCh38. 5 run(s), 5 experiment(s), 5 alignment(s). Part of BLUEPRINT (September 2016).

  Dataset EGAD00001002918

• 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

• ICGC PCAWG Dataset: PRAD-CA_PCAWG_WGS_BWA

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

  Dataset EGAD00001002128

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

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

  Dataset EGAD00001004093

• WGS of T-cell and NK-cell lymphoma for ICGC (NKTL-SG)

  WGS of T-cell and NK-cell lymphoma The tumor samples were sequenced with Illumina HiSeq 2500 platform and the resulting FASTq files have been uploaded.

  Dataset EGAD00001003271

• NKI-AvL OpACIN DNA-seq of stage III melanoma patients

  The dataset “NKI-AvL OpACIN DNA-seq of stage III melanoma patients" includes 2 x 18 normal and 2 x 18 tumor FASTQ files from paired-end whole exome sequencing on Illumina HiSeq2500 for 18 stage III melanoma patients.

  Dataset EGAD00001004217

• Exploration of neuroblastoma xenograft models for tumor extracellular RNA profiling in murine blood plasma

  Total RNA sequencing (SMARTer Stranded Total RNA-Seq Kit v2) data of extracellular RNA (exRNA) from liquid biopsies of neuroblastoma xenograft models.

  Dataset EGAD00001010905

• Bulk RNA from sorted CD8+ T cells after 48h co-culture with human Mito-DsRed MSCs.

  For human samples, total cellular RNA was isolated from post-sorted Mito+ and Mito CD8+ cells using the RNeasy Mini Kit (Qiagen). Stranded RNA libraries were created using SMARTSeq Stranded.

  Dataset EGAD00001011082

• ICGC PCAWG Dataset: GACA-CN_PCAWG_WGS_BWA

  ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: GACA-CN.

  Dataset EGAD00001003132