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• DAC for genentech GBC study

  Dac EGAC00001001155

• Department for BioMedical Research, University of Bern

  Dac EGAC00001001457

• DAC for Gastric Adenocarcinoma Heterogeneity study

  Dac EGAC00001001649

• Data Access Committee for IMBA

  Dac EGAC00001001690

• Data Access Committee for data from EGAS00001005174

  Dac EGAC00001002059

• Data Access Committee for data from EGAS00001005395

  Dac EGAC00001002183

• Data Access Committee for PPIL4 Paper

  Dac EGAC00001002301

• Data Access Committee for Massim study

  Dac EGAC00001002522

• Data Access Committee for Institut Curie

  Dac EGAC00001002711

• Data Access Committee for Pediatric Medulloblastoma

  Dac EGAC00001002896

• Institute for Surgical Pathology

  Dac EGAC00001002949

• Data Access Commitee for MNP2

  Dac EGAC00001003033

• DAC for Karolinska Institute REM Lab

  Dac EGAC00001003142

• DAC for Kotsch/Lukassen/Conrad labs

  Dac EGAC00001003464

• Data Access Committee for data from EGAS00001002864

  Dac EGAC00001003487

• Data Access Committee for data from EGAS00001007832

  Dac EGAC00001003500

• Data Access Committee for data from EGAS00001007819

  Dac EGAC00001003501

• Data Access Committee for data from EGAS00001007904

  Dac EGAC00001003512

• Data Access Committee for data from EGAS00001008107

  Dac EGAC00001003568

• UCL Centre for Longitudinal Studies

  Dac EGAC00001001041

• BAP1 Project

  For our BAP1 manuscript

  Dac EGAC50000000006

• EGAD00010000608

  SNP6 data for seminoma samples

  Dataset EGAD00010000608

• PEDS-PLAN - Pediatric Precision Laboratory Advanced Neuroblastoma Therapy

  A multi-center clinical trial for newly diagnosed high-risk neuroblastoma patients. Molecular tumor boards selected one of six targeted agents based on tumor-normal whole exome sequencing and tumor RNA sequencing data.

  Study phs002303

• Genome-wide association scan in psoriasis

  To identify novel susceptibility loci for psoriasis, we undertook a genome-wide association scan of of 594,224 SNPs in 2,622 individuals with psoriasis and 5,667 controls.

  Study EGAS00000000108

• cfDNA sWGS BAM — Breast cancer stage II-III (HR+/HER2−)

  Plasma cfDNA sWGS for breast cancer patients (HR+/HER2−, stage II–III), blood drawn pre-operatively (no neoadjuvant), Centre Léon Bérard/MyProbe (France). Libraries: DSP and/or SSP as recorded. Sequencing by IntegraGen (2022–2024); alignment to GRCh38 with BWA-MEM; BAMs sorted/indexed; primary mapped reads only (see analysis metadata for exact filters/MAPQ). Controlled access.

  Dataset EGAD50000001877

• Bulk ATAC data

  Bulk ATAC libraries were generated for patient samples A.1, A.3, A.5, A.6, A.7, A.11, A.12, A.13 and A.15. For each patient a library of CD3- cells (myeloid cells, considered tumor cells) and CD3+ cells (T cells, considered healthy) were generated.

  Dataset EGAD00001010188

• Mucosal 16S sequencing data

  16S-V4 rRNA gene sequence data for intestinal biopsies from NCT02749630 trial participants. Biopsies from patients were collected at screening, day 30, and day 85 and prepared for 16SV4 rRNA gene sequencing.

  Dataset EGAD00001008843

• RNA-Seq data for manuscript titled: Multi-omic features of oesophageal adenocarcinoma in patients treated with preoperative neoadjuvant therapy

  RNA-Seq data for manuscript titled: Multi-omic features of oesophageal adenocarcinoma in patients treated with preoperative neoadjuvant therapy

  Dataset EGAD00001008656

• single-cell RNAseq FASTq files for three muscle-invasive bladder tumors

  single-cell RNAseq FASTq files for three muscle-invasive bladder tumors

  Dataset EGAD00001008001

• Genomic and transcriptomic data of glioma specimens

  Dataset consists of 207 glioma samples of WHO grades II, III and IV. Dataset consists 182 tumor derived genomic data of ~700 cancer-related and epigenetic-related genes with matched blood samples for 48 specimens. Dataset also consists transcriptomic data for 105 specimens. In total 335 bam files were deposited.

  Dataset EGAD00001006299

• aCGH CNV detection by CNsolidate for 6,827 DDD probands

  aCGH CNV detection by CNsolidate for 6,827 DDD probands

  Dataset EGAD00001005728

• Sequencing files for "A Unifying Paradigm for Transcriptional Heterogeneity and Squamous Features in Pancreatic Ductal Adenocarcinoma."

  Files from DNA and RNA sequencing from primary tumors and metastases from pancreatic cancer patients along with matched normal tissues.

  Dataset EGAD00001005519

• RNAseq files (dataset 2 of 2) for Mullighan PAX5_B-ALL

  RNAseq files (dataset 2 of 2) for Mullighan PAX5_B-ALL paper titled "PAX5-driven Subtypes of B-cell Acute Lymphoblastic Leukemia"

  Dataset EGAD00001004463

• RNAseq files (dataset 1 of 2) for Mullighan PAX5_B-ALL

  RNAseq files (dataset 1 of 2) for Mullighan PAX5_B-ALL paper titled "PAX5-driven Subtypes of B-cell Acute Lymphoblastic Leukemia"

  Dataset EGAD00001004461

• WXS files for paper titled 'Genomic Landscape of Pediatric Myelodysplastic Syndromes'

  Paired whole exome sequencing for 32 primary MDS, 14 MDS/MPN, and 8 AML-MRC cases (total = 54). Normal comparator genomic DNA was extracted from lymphocytes purified by flow cytometry. Bulk myeloid cells were used as a source of tumor gDNA. Files uploaded are mapped BAM files.

  Dataset EGAD00001003781

• Transcriptome/Exome for glioblastoma intra-tumoral heterogeneity

  Total of 49 tumor specimens from 20 patients were subjected for whole-exome and/or whole-transcriptome sequencing including matched normal/blood. Tumor samples are acquired based on 4 categories; 1) locally adjacent tumors, 2) multifocal/multicentric tumors, 3) 5-ALA (+/-) tumors and 4) Longitudinal tumors.

  Dataset EGAD00001002248

• Sequencing Data for Sample 51_Hf01_BlCM_Ct

  Sequencing Data for DEEP Paper: "reChIP-seq reveals widespread bivalency of H3K4me3 and H3K27me3 in CD4+ memory T-Cells" Sample: 51_Hf01_BlCM_Ct (human, female, Blood, CD4+ central memory cell, normal control) Sequencing types are: total RNA, Whole Genome Bisulfite, ChipSeq (H3K27ac, H3K9me3, H3k36me3, H3K4me1, H3k27me3, H3K4me3, Input), reChipSeq (H3K27me3, H3K4me3)

  Dataset EGAD00001002255

• BLUEPRINT release August 2016, RNA-Seq for macrophage - T=6days LPS, on genome GRCh38

  RNA-Seq data for 4 macrophage - T=6days LPS sample(s). 4 run(s), 4 experiment(s), 4 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816

  Dataset EGAD00001002337

• BLUEPRINT release August 2015, DNase-Hypersensitivity for alternatively activated macrophage, on genome GRCh38

  DNase-Hypersensitivity data for 1 alternatively activated macrophage sample(s). 1 run(s), 1 experiment(s), 1 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_dnaseseq_analysis_20150820

  Dataset EGAD00001001545

• BLUEPRINT release August 2016, RNA-Seq for macrophage - T=6days B-glucan, on genome GRCh38

  RNA-Seq data for 4 macrophage - T=6days B-glucan sample(s). 4 run(s), 4 experiment(s), 4 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816

  Dataset EGAD00001002522

• BLUEPRINT release August 2016, RNA-Seq for macrophage - T=6days untreated, on genome GRCh38

  RNA-Seq data for 4 macrophage - T=6days untreated sample(s). 4 run(s), 4 experiment(s), 4 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816

  Dataset EGAD00001002457

• BLUEPRINT release August 2016, DNase-Hypersensitivity for alternatively activated macrophage, on genome GRCh38

  DNase-Hypersensitivity data for 2 alternatively activated macrophage sample(s). 2 run(s), 2 experiment(s), 2 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_dnaseseq_analysis_20160816

  Dataset EGAD00001002481

• BLUEPRINT release January 2015, Bisulfite-Seq for Acute promyelocytic leukemia

  Bisulfite-Seq data for 3 Acute promyelocytic leukemia sample(s). 24 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811

  Dataset EGAD00001001167

• BLUEPRINT release January 2015, Bisulfite-Seq for Acute myeloid leukemia

  Bisulfite-Seq data for 1 Acute myeloid leukemia sample(s). 18 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811

  Dataset EGAD00001001162

• BLUEPRINT release January 2015, DNase-Hypersensitivity for CD34-negative, CD41-positive, CD42-positive megakaryocyte cell

  DNase-Hypersensitivity data for 1 CD34-negative, CD41-positive, CD42-positive megakaryocyte cell sample(s). 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_dnaseseq_analysis_20140811

  Dataset EGAD00001001161

• BLUEPRINT release January 2015, Bisulfite-Seq for Multiple myeloma

  Bisulfite-Seq data for 2 Multiple myeloma sample(s). 16 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811

  Dataset EGAD00001001152

• BLUEPRINT release January 2015, DNase-Hypersensitivity for CD14-positive, CD16-negative classical monocyte

  DNase-Hypersensitivity data for 5 CD14-positive, CD16-negative classical monocyte sample(s). 5 run(s), 5 experiment(s), 5 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_dnaseseq_analysis_20140811

  Dataset EGAD00001001130

• BLUEPRINT release August 2014, DNase-Hypersensitivity for CD34-negative, CD41-positive, CD42-positive megakaryocyte cell

  DNase-Hypersensitivity data for 1 CD34-negative, CD41-positive, CD42-positive megakaryocyte cell sample(s). 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_dnaseseq_analysis_20140811

  Dataset EGAD00001000942

• BLUEPRINT release August 2014, Bisulfite-Seq for Multiple myeloma

  Bisulfite-Seq data for 2 Multiple myeloma sample(s). 16 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811

  Dataset EGAD00001000934

• BLUEPRINT release August 2014, DNase-Hypersensitivity for CD14-positive, CD16-negative classical monocyte

  DNase-Hypersensitivity data for 5 CD14-positive, CD16-negative classical monocyte sample(s). 5 run(s), 5 experiment(s), 5 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_dnaseseq_analysis_20140811

  Dataset EGAD00001000905