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• 10x Genomics Single Cell Gene Expression for SA1091AX1XB01790

  10x Genomics Single Cell Gene Expression for High grade serous ovarian carcinoma patient-derived xenograft SA1091 passage 1

  Dataset EGAD00001009130

• 10x Genomics Single Cell Gene Expression for SA1093CX1XB01917

  10x Genomics Single Cell Gene Expression for High grade serous ovarian carcinoma patient-derived xenograft SA1093 passage 1

  Dataset EGAD00001009129

• 10x Genomics Single Cell Gene Expression for SA1053FX1XB01611

  10x Genomics Single Cell Gene Expression for High grade serous ovarian carcinoma patient-derived xenograft SA1053 passage 1

  Dataset EGAD00001009128

• 10x Genomics Single Cell Gene Expression for SA1052BX1XB01516

  10x Genomics Single Cell Gene Expression for High grade serous ovarian carcinoma patient-derived xenograft SA1052 passage 1

  Dataset EGAD00001009127

• 10x Genomics Single Cell Gene Expression for SA1050DX1XB01437

  10x Genomics Single Cell Gene Expression for High grade serous ovarian carcinoma patient-derived xenograft SA1050 passage 1

  Dataset EGAD00001009126

• 10x Genomics Single Cell Gene Expression for SA1050FX1XB01446

  10x Genomics Single Cell Gene Expression for High grade serous ovarian carcinoma patient-derived xenograft SA1050 passage 1

  Dataset EGAD00001009125

• 10x Genomics Single Cell Gene Expression for SA604X8XB02164

  10x Genomics Single Cell Gene Expression for Triple negative breast cancer patient-derived xenograft SA604 passage 8

  Dataset EGAD00001009118

• 10x Genomics Single Cell Gene Expression for SA604X6XB01979

  10x Genomics Single Cell Gene Expression for Triple negative breast cancer patient-derived xenograft SA604 passage 6

  Dataset EGAD00001009117

• 10x Genomics Single Cell Gene Expression for SA1054

  10x Genomics Single Cell Gene Expression for Telomerase immortalized breast epithelium cell line 184-hTERT-22 L9 83.86

  Dataset EGAD00001009113

• 10x Genomics Single Cell Gene Expression for SA1056

  10x Genomics Single Cell Gene Expression for Telomerase immortalized breast epithelium cell line 184-hTERT-22 L9 116.126

  Dataset EGAD00001009112

• 10x Genomics Single Cell Gene Expression for SA1188

  10x Genomics Single Cell Gene Expression for Telomerase immortalized breast epithelium cell line 184-hTert L9 116.66

  Dataset EGAD00001009114

• 10x Genomics Single Cell Gene Expression for SA604X7XB02089

  10x Genomics Single Cell Gene Expression for Triple negative breast cancer patient-derived xenograft SA604 passage 7

  Dataset EGAD00001009119

• 10x Genomics Single Cell Gene Expression for SA609X6XB01899

  10x Genomics Single Cell Gene Expression for Triple negative breast cancer patient-derived xenograft SA609 passage 6

  Dataset EGAD00001009120

• 10x Genomics Single Cell Gene Expression for SA1049AX1XB01417

  10x Genomics Single Cell Gene Expression for High grade serous ovarian carcinoma patient-derived xenograft SA1049 passage 1

  Dataset EGAD00001009121

• 10x Genomics Single Cell Gene Expression for SA1052DX1XB01519

  10x Genomics Single Cell Gene Expression for High grade serous ovarian carcinoma patient-derived xenograft SA1052 passage 1

  Dataset EGAD00001009122

• 10x Genomics Single Cell Gene Expression for SA1053EX1XB01608

  10x Genomics Single Cell Gene Expression for High grade serous ovarian carcinoma patient-derived xenograft SA1053 passage 1

  Dataset EGAD00001009123

• 10x Genomics Single Cell Gene Expression for SA1051AX1XB01452

  10x Genomics Single Cell Gene Expression for High grade serous ovarian carcinoma patient-derived xenograft SA1051 passage 1

  Dataset EGAD00001009124

• 10x Genomics Single Cell Gene Expression for SA535X6XB03099

  10x Genomics Single Cell Gene Expression for Triple negative breast cancer patient-derived xenograft SA535 passage 6

  Dataset EGAD00001009116

• 10x Genomics Single Cell Gene Expression for SA535X4XB05462

  10x Genomics Single Cell Gene Expression for Triple negative breast cancer patient-derived xenograft SA535 passage 4

  Dataset EGAD00001009115

• 10x Genomics Single Cell Gene Expression for SA1055

  10x Genomics Single Cell Gene Expression for Telomerase immortalized breast epithelium cell line 184-hTERT-22 L9 112.109

  Dataset EGAD00001009111

• Tumour sample for patient SA530

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA530

  Dataset EGAD00001009191

• Tumour sample for patient SA404

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA404

  Dataset EGAD00001009190

• Tumour sample for patient SA402

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA402

  Dataset EGAD00001009189

• Tumour sample for patient SA398

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA398

  Dataset EGAD00001009188

• Tumour sample for patient SA395

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA395

  Dataset EGAD00001009187

• Tumour sample for patient SA394

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA394

  Dataset EGAD00001009186

• Tumour sample for patient SA287

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA287

  Dataset EGAD00001009185

• Tumour sample for patient SA283

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA283

  Dataset EGAD00001009184

• Tumour sample for patient SA279

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA279

  Dataset EGAD00001009183

• Tumour sample for patient SA276

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA276

  Dataset EGAD00001009182

• Tumour sample for patient SA275

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA275

  Dataset EGAD00001009181

• Tumour sample for patient SA274

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA274

  Dataset EGAD00001009180

• Tumour sample for patient SA272

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA272

  Dataset EGAD00001009179

• Tumour sample for patient SA219

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA219

  Dataset EGAD00001009178

• Tumour sample for patient SA218

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA218

  Dataset EGAD00001009177

• A96177B

  Whole genome sequencing for single cells for library A96177B 683 samples; filetype=bam

  Dataset EGAD00001008244

• A96174B

  Whole genome sequencing for single cells for library A96174B 1447 samples; filetype=bam

  Dataset EGAD00001008242

• A96165A

  Whole genome sequencing for single cells for library A96165A 779 samples; filetype=bam

  Dataset EGAD00001008239

• A96155B

  Whole genome sequencing for single cells for library A96155B 1028 samples; filetype=bam

  Dataset EGAD00001008236

• A96145A

  Whole genome sequencing for single cells for library A96145A 642 samples; filetype=bam

  Dataset EGAD00001008232

• A95732B

  Whole genome sequencing for single cells for library A95732B 655 samples; filetype=bam

  Dataset EGAD00001008231

• A95707A

  Whole genome sequencing for single cells for library A95707A 1359 samples; filetype=bam

  Dataset EGAD00001008228

• A95664B

  Whole genome sequencing for single cells for library A95664B 630 samples; filetype=bam

  Dataset EGAD00001008227

• RNA-Seq dataset for Genomic rearrangements in Pediatric Cancer

  RNA-Seq data for systematic gene fusion detection in Pediatric Cancer

  Dataset EGAD00001008152

• A96233A

  Whole genome sequencing for single cells for library A96233A 637 cells; filetype=bam

  Dataset EGAD00001007622

• A95730A

  Whole genome sequencing for single cells for library A95730A 739 cells; filetype=bam

  Dataset EGAD00001007614

• A108833B

  Whole genome sequencing for single cells for library A108833B 866 cells; filetype=bam

  Dataset EGAD00001007594

• A108735A

  Whole genome sequencing for single cells for library A108735A 714 cells; filetype=bam

  Dataset EGAD00001007593

• A96114A

  Whole genome sequencing for single cells for library A96114A 798 cells; filetype=bam

  Dataset EGAD00001007615

• RNA-sequencing of meningiomas for integrative molecular classification.

  RNA-sequencing of meningiomas for integrative molecular classification.

  Dataset EGAD00001007494

• EGAD00010000730

  WTCCC2 Psychosis Endophenotype samples from UK, Germany, Holland, Spain and Australia using the Affymetrix 6.0 array

  Dataset EGAD00010000730

• Balanced Brain Tumour Whole Genome Sequencing

  We propose to definitively characterise the somatic genetics of a number of pediatric malignant tumours including ependymoma, high grade glioma and central nervous system primitive neurectodermal tumours through generation of comprehensive catalogues of somatic mutations by high coverage genome sequencing.

  Dataset EGAD00001000369

• Sequencing data of the CTSC gene after WGS of samples from individuals with PLS

  The sequencing data of the CTSC gene after whole genome sequencing of blood samples from two individuals with Papillon-Lèfevre Syndrome.

  Dataset EGAD00001006961

• Single-cell whole-genome sequencing reveals convergent evolution in Burkitt lymphoma

  This depository contains the raw BAM/CRAM files used in the manuscript "Single-cell whole-genome sequencing reveals convergent evolution in Burkitt lymphoma" Steemers et al. (2026). This includes: - 332 PTA-based single-cell WGS samples (~15X depth) - 7 bulk tumour samples (~30X depth) with matched germline samples (~30X depth) - 14 bulk tumour samples seqeunced by the Princess Maxima Centre diagnostics department (~105X depth) with matched germline samples (~35X depth)

  Study EGAS50000001681

• Mutational_Signatures_of_relapse_in_rectal_cancer_FFPE_samples_in_the_CR07_clinical_trial

  The CRO7 clinical trial recruited patients with clinically operable rectal adenocarcinoma. Patients were randomized to either pre-operative short course surgery followed by chemo-radiotherapy only in those patients at high risk of local relapse. Patients in both arms the received standard %-FU based adjuvant chemotherapy as per local policy. We intend to use FFPE derived DNA from the primary tumours to identify patterns of mutations or copy number alterations that are predictive of local or distant relapse.

  Study EGAS00001000651

• RNAseq data

  RNAseq FASTq files from 797 tumors from AVANT. Sequencing libraries were generated with the TruSeq Stranded Total RNA kit (Illumina) following ribosomal RNA (rRNA) depletion with the Ribo-Zero Gold kit (Illumina). The libraries were sequenced on the HiSeq4000 (Illumina) with a sequencing protocol of 75 bp paired-end sequencing. Note: 10 samples used in the original publication were excluded from this upload due to regulations from the Human Genetics Resources Administration of China (HGRAC).

  Dataset EGAD00001009728

• Familial Melanoma Sequencing

  In this experiment we have sequenced the exome of 15 individuals from eight families who have familial melanoma. By sequencing the exome we hope to be able to identify new genes that are associated with this disease.

  Study EGAS00001000017

• Discovery_of_resistance_mechanisms_to_the_BRAF_inhibitor_vemurafenib_in_metastatic_BRAF_mutant_melanoma

  Discovery of resistance mechanisms to the BRAF inhibitor vemurafenib in metastatic BRAF mutant melanoma by massively-parallel sequencing of tumour samples. Comparison of genomic characteristics of pretreatment ‘sensitive’ to recurrence ‘resistant’ tumours to identify the genetics of drug resistance.

  Study EGAS00001000551

• BELOB: Ribo-minus RNA-seq data corresponding to 96x GBM samples from the BELOB trial.

  Ribo-minus RNA-seq data corresponding to 96x GBM samples from the BELOB trial.

  Study EGAS00001004570

• The genomic landscape of acute lymphoblastic leukemia with intrachromosomal amplification of chromosome 21

  Use scRNA-seq data from 4 iAMP21 patients to study the clonal evolution of iAMP21.

  Study EGAS00001006577

• Spatial

  This dataset contains the raw sequencing data (Runs) from all of the 10x Genomics single-cell Visium Experiments, as well as the corresponding imaging data (Analyses).

  Dataset EGAD00001009821

• Genomic and Epigenomic Features of Primary and Recurrent Hepatocellular Carcinomas

  Intratumor heterogeneity and divergent clonal lineages within and among primary and recurrent hepatocellular carcinomas (HCCs) produce challenges to patient management. We investigated genetic and epigenetic variations within liver tumors, among hepatic lesions, and between primary and relapsing tumors. We performed whole-genome, whole-exome, or targeted capture sequencing analyses HCC specimens collected from multiple tumor regions and matched initial and recurrent tumors to obtain a systematic evaluation of intra- and intertumor genetic heterogeneity in HCC samples and to identify genetic changes associated with tumor progression and recurrence.

  Study EGAS00001002094

• The WID-BC-index identifies women with primary poor prognostic breast cancer based on DNA methylation in cervical samples

  A surrogate marker based on the epigenome that captures these components in easily accessible epithelial tissue could potentially identify women at risk. The WID-BC-index identifies women with breast cancer based on a DNA methylation signature derived from cervical smear samples.

  Study EGAS00001005055

• Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A96213A

  Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 522 samples; filetype=bam

  Dataset EGAD00001004771

• LBC1921 bam files

  297 members of the LBC1921 were sequenced using the Illumina HiSeq X platform. This dataset contains the bam files.

  Dataset EGAD00001011667

• analysis of T cell receptor repertoirs

  Full information about the T cell receptor (CR) variable regions found in the sequences of the vdj region. Columns: barcode is_cell contig_id high_confidence length chain v_gene d_gene j_gene c_gene full_length productive cdr3 cdr3_nt reads umis raw_clonotype_id raw_consensus_id

  Dataset EGAD00001008109

• The Dutch retinoblastoma research team from the VU University medical center

  Dac EGAC00001000431

• NABEC: North American Brain Expression Consortium

  This study utilized neurologically normal control samples deposited in North American Brain Expression Consortium (NABEC). This top-level study, phs001300, makes available all phenotype data of the NABEC study participants.In addition, molecular data from the substudies, listed above, are available.

  Study phs001300

• A brain precursor atlas reveals the acquisition of developmental-like states in adult cerebral tumours

  We generated a single-cell RNA-seq atlas capturing over 100,000 cells spanning all stages of the mouse cerebral development. By examining data from over 100 cerebral tumour samples, our study reveals that, despite the phenotypic/genotypic differences between the tumour types, they are all comprised of developmental sublineages that map most closely to embryonic or juvenile stages of development.

  Dataset EGAD00001008746

• 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

• ctDNA sample level analysis

  This table summarizes Guardant 360 ctDNA variant summary statistics including frequency of variant types for each sample included in this analysis.

  Dataset EGAD50000001341

• 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

• Raw count matrix for 418 baseline samples

  Count matrix from 418 pre-treatment (Ven-Obi or Clb-Obi) CD19+ B cells

  Dataset EGAD00001009501

• 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

• 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 - MGI CoolMPS short-read sequencing

  MGI CoolMPS short-read sequencing data for individual HV31 generated using DNA from peripheral blood mononuclear cells, to a sequencing depth of ~57×.

  Dataset EGAD00001007048

• HV31 - MGI standard short-read sequencing

  MGI standard short-read sequencing data for individual HV31 generated using DNA from peripheral blood mononuclear cells, to a sequencing depth of ~57×.

  Dataset EGAD00001007044

• 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

• 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

• Genomic insights into the population history of the Resande or Swedish Travellers

  Study EGAS00001006176

• Transcriptomic characterization of the histopathological growth patterns in breast cancer liver metastases

  Characterizing transcriptommic profiles of the two main histopathological growth patterns in liver metastases in patients with breast cancer.

  Study EGAS50000000225

• LBC1936 bam files

  1075 members of the LBC1936 were sequenced using the Illumina HiSeq X platform. This dataset contains the bam files.

  Dataset EGAD50000001740

• GCAT| WGS Structural Variants Catalog V1

  This resource contains the SV annotations using the AnnotSV tool. The description of annotations can be found in AnnotSV web page https://lbgi.fr/AnnotSV/ or GCAT-BSC web page: http://cg.bsc.es/GCAT_BSC_iberianpanel

  Dataset EGAD00010002152

• MCL Multiome

  This dataset contains the raw sequencing data (Runs) from the 10x Genomics single-cell Multiome Experiments which belong to the MCL group

  Dataset EGAD00001009819

• Data Access Committee of the Medical Faculty of the University of Basel (MF-DAC)

  Dac EGAC00001002981

• The genomic imprint of cancer therapies helps timing the formation of metastases

  Study EGAS00001003416

• The EMC-HEMA-AML-DNMT3A data access committee controlling the access to DNMT3A-mutated AML

  Dac EGAC00001003511

• Multi Omics of glioma in the the Chinese Glioma Genome Atlas (CGGA) project

  Study EGAS00001004729

• The genomic landscape of acute lymphoblastic leukemia with intrachromosomal amplification of chromosome 21

  Use single cell whole genome sequencing data from one iAMP21 patient SJBALL021901 to study the clonal evolution of iAMP21.

  Study EGAS00001006796

• CITE-seq

  This dataset contains the raw sequencing data (Runs) from all of the 10x Genomics single-cell CITE-seq Experiments, as well as the demultiplexed cell-donor identities matrices which were generated with Vireo (Analysis).

  Dataset EGAD00001009820

• Pre-treatment PD-L1 staining on tumor samples (n=24)

  Data from NABUCCO cohort 1 (NCT03387761). This dataset includes the pre-treatment PD-L1 staining on tumor samples (n=24). Details about the PD-L1 staining can be found on the paper (https://doi.org/10.1038/s41591-020-1085-z)

  Dataset EGAD00001006856

• WGS reads mapping within the IG loci

  Previously unpublished WGS reads mapping within the IG loci used in the benchmark of IgCaller.

  Dataset EGAD00001006032

• Longitudinal RNA-seq in a twin cohort

  The dataset consists of 232 RNA-seq samples (whole blood) obtained from healthy female from the TwinsUK adult registry cohort. The samples were obtained at two time points separated on average by 22 months.

  Dataset EGAD00001002068

• Targeted sequencing of brain expressed miRNA genes

  As regulators of gene expression, microRNAs (miRNAs) are likely to play an important role in the development of disease. In this study we present a large-scale strategy to identify miRNAs with a role in the regulation of neuronal processes by screening 289 brain expressed miRNAs. Thereby we found variant rs7861254 located near the MIR204 gene to be significantly associated with schizophrenia. This variant resulted in reduced expression of miR-204 in neuronal-like SH-SY5Y cells.

  Study EGAS00001001607

• Genome and transcriptome sequence data from a pancreatic adenocarcinoma patient

  Genome and transcriptome sequence data from a pancreatic adenocarcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001011035

• Genome and transcriptome sequence data from a liposarcoma patient

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

  Dataset EGAD00001011032

• Genome and transcriptome sequence data from a urachal adenocarcinoma patient

  Genome and transcriptome sequence data from a urachal adenocarcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001011031

• Genome and transcriptome sequence data from a pancreatic adenocarcinoma patient

  Genome and transcriptome sequence data from a pancreatic adenocarcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001011030

• Genome and transcriptome sequence data from a colorectal carcinoma patient

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

  Dataset EGAD00001011029