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• Breast Cancer Association Consortium Data Access Coordinating Committee

  Data access committee for the Breast Cancer Association Consortium (BCAC).

  Dac EGAC50000000824

• The INFORM Precision Medicine Study for High-Risk Pediatric Malignancies

  Study EGAS00001005112

• Cancer Research UK Cambridge Institute

  A department of the University of Cambridge and Cancer Research UK funded Institute

  Dac EGAC50000000683

• The effects of bioinformatics preprocessing on cell-free DNA analysis

  The dataset contain 20 lung cancer and 20 healthy control cfDNA samples from plasma sequenced using 150bp PE sequencing.

  Dataset EGAD50000000213

• A fast, affordable and minimally-invasive diagnostic test for Cancer of Unknown Primary (CUP) using DNA methylation profiling

  CUP diagnosis on FFPE tissue and liquid biopsies (blood, pleural and peritoneal effusions) using cfRRBS (cell-free reduced representation bisulfite sequencing), a technique that allows for identification of the methylation profile starting from minimal amounts of highly fragmented DNA.

  Study EGAS50000000257

• Comprehensive genomic characterization of early stage bladder cancer - shallow whole genome sequencing data

  For this project about non-muscle invasive bladder cancer (NMIBC), we analysed shallow WGS data from 362 patients. The dataset is composed of 392 BAM files: 362 tumor samples, 15 female normal samples and 15 male normal samples.

  Study EGAS50000000513

• Single cell RNA sequencing of co-culture of human organoids with polarized pro-inflammatory (M1) or anti-inflammatory (M2) macrophages

  Human intestinal organoids co-cultured with pro-inflammatory (M1) or anti-inflammatory (M2) human macrophages for 48 hours. 3 days after the co-culture alive cells were sorted and processed for single cell RNA sequencing

  Study EGAS50000000467

• Raw and processed Spatial Transcriptomics data of Choroid Plexus Tumours

  This dataset contains raw sequencing and processed data of spatially resolved transcriptomes. The data were generated with 10X Visium probe-based assay of FFPE tissues of 14 CPT tumour resections and 2 non-neoplastic reference samples. Raw data contain two-lane fastq files of the sequencing. Processed data contain alinged and filteres count matrices as well as positional files as generated by 10x SpaceRanger

  Dataset EGAD50000002319

• Raw and processed snRNAseq data of Choroid Plexus Tumors

  This dataset contains raw sequencing and processed data of single nuclei transcriptomes. The data were generated with 10x chromium probe-based single-nucleus assay on FFPE tissues of 43 Choroid Plexus Tumour resections and 12 non-neoplastic fetal and adult ChP resections. Raw data contain BAM files of the sequencing. Processed data contain count matrices as generated by 10x CellRanger for raw and filtered running options.

  Dataset EGAD50000002320

• Genome-wide association data on male-pattern baldness

  The study comprises 1000Genomes imputed data for 581 MPB cases and 416 male controls. Cases are selected for age<40 and Hamilton-Norwood grade V-VII. Control include 270 males >60 years no signs of AGA (Hamilton-Norwood grade I).

  Study EGAS00001001354

• Cell type-specific transcriptomics of esophageal adenocarcinoma as a scalable alternative for single cell transcriptomics

  We developed a protocol for the separation of esophageal carcinoma tissue into leukocytes (using CD45 as a marker), epithelial cells (EpCAM), and fibroblasts (two out of PDGFRA, CD90, anti-fibroblast) by fluorescence-activated cell sorting followed by RNA-sequencing

  Study EGAS00001004053

• Colon Cancer Organoid Cultures and Tumors Whole Exome Sequencing Data

  Five hundred fifty nanograms of genomic DNA were input for library preparation after fragmentation by Covaris S2, following the KAPA Hyper Prep Kit (KR0961-V1.14) protocols, with selection for a library size range of 250-450 bp. Three hundred nanograms per library DNA each from 12 samples were normalized and combined into a single pool for exome capture using the xGen Lockdown Probes and Reagents based on their standard protocols

  Dataset EGAD00001005754

• August 2020 data update (fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium.

  August 2020 data update (fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies (Canadian Epigenetics, Environment and Health Research Consortium), Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001006383

• scRNA-seq of relapsed/refractory multipe myeloma with 10x Chromium (3´ v2)

  This dataset includes 87 scRNA-seq samples of bone marrow aspirates of 20 relapsed/refractory patients generated with the 3´(v2) kit of the 10x Chromium platform. Bone marrow cells have been sorted using CD138 +/- fractions using magnetic beads for plasma cell enrichment and processed independently. For 14/20 patients multiple treatment timepoints are available that includes samples before treatment and at relapse during treatment.

  Dataset EGAD00001006903

• August 2019 data update (fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium.

  August 2019 data update (fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies (Canadian Epigenetics, Environment and Health Research Consortium), Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001005335

• BLUEPRINT release August 2016, Bisulfite-Seq for mesenchymal stem cell of the bone marrow, on genome GRCh38

  Bisulfite-Seq data for 2 mesenchymal stem cell of the bone marrow sample(s). 39 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_bisulphite_analysis_CNAG_20160816

  Dataset EGAD00001002519

• May 2019 data update (fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium.

  May 2019 data update (fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies (Canadian Epigenetics, Environment and Health Research Consortium), Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001005060

• Single-nucleus Transcriptome of Down Syndrome Brains (short-read)

  29 DS and Control brain samples were prepared using the 10X Genomics Single Cell 3' v3 kit. The cDNA libraries were sequenced on an Illumina Novaseq 6000.

  Dataset EGAD00001008287

• Single cell transcriptomics of hESC-derived midbrain dopaminergic neurons generated by a new human development-based protocol

  Single cell RNA-seq from D0,D11,D16,D21,D28 of dopamingeric differentiation from hESCs cell lines H9 and HS980 using current protocols. Different time points along the differentiation for each cell line were multiplexed using BD™ Single-Cell Multiplexing Kit for use with the 10x Chromium™ Single Cell 3’ Reagent Kit v2.

  Dataset EGAD00001008834

• Chronic lymphocytic leukemia IGHV somatic hypermutation detection by targeted capture next-generation sequencing

  FASTQ and BAM files for 46 samples (consisting of 35 samples for patients diagnosed with CLL, 5 samples consisting of a dilution series of patient DNA, and 6 samples of cell lines and dilutions involving the cell lines) from targeted capture next-generation sequencing from the LySeq panel. Libraries were sequenced on either Illumina HiSeq 2500 (LySeq66 PoP, R1-3) or Illumina NovaSeq 6000 (LySeq66 Validation Round).

  Dataset EGAD00001009828

• September 2016 data update (bam/fastq/vcf) for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium.

  September 2016 data update (bam/fastq/vcf) for reference epigenomes generated at Centre for Epigenome Mapping Technologies (Canadian Epigenetics, Environment and Health Research Consortium), Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001002724

• Udated data for October 2017 data release for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium.

  October 2017 data update (bam/fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies (Canadian Epigenetics, Environment and Health Research Consortium), Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001003906

• January 2018 data update (bam/fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium.

  January 2018 data update (bam/fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies (Canadian Epigenetics, Environment and Health Research Consortium), Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001003962

• June 2017 data update (bam/fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium.

  June 2017 data update (bam/fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies (Canadian Epigenetics, Environment and Health Research Consortium), Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001003414

• RNA sequencing of high hyperdiploid and ETV6/RUNX1-positive pediatric acute lymphoblastic leukemia

  RNA-sequencing data of pediatric B-cell precursor acute lymphoblastic leukemia, including 18 high hyperdiploid cases and 9 ETV6/RUNX1-positive cases. Sequencing libraries were constructed using the Human Ribo-Zero rRNA Removal Kit (Illumina, San Diego, CA) and sequenced on an Illumina NextSeq 500. RNA sequencing data were processed using the TCGA mRNA-seq pipeline (https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline/#mrna-analysis-pipeline).

  Dataset EGAD00001004176