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• BLUEPRINT release August 2016, ChIP-Seq for germinal center B cell, on genome GRCh38

  ChIP-Seq data for 4 germinal center B cell sample(s). 24 run(s), 22 experiment(s), 22 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_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002442

• BLUEPRINT release August 2016, ChIP-Seq for immature conventional dendritic cell - GM-CSF_IL4_T=6_days, on genome GRCh38

  ChIP-Seq data for 3 immature conventional dendritic cell - GM-CSF_IL4_T=6_days sample(s). 20 run(s), 20 experiment(s), 20 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_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002485

• BLUEPRINT release August 2016, ChIP-Seq for adult endothelial progenitor cell, on genome GRCh38

  ChIP-Seq data for 2 adult endothelial progenitor cell sample(s). 16 run(s), 14 experiment(s), 14 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_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002487

• BLUEPRINT release August 2016, ChIP-Seq for endothelial cell of umbilical vein (resting), on genome GRCh38

  ChIP-Seq data for 2 endothelial cell of umbilical vein (resting) sample(s). 13 run(s), 13 experiment(s), 13 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_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002488

• What is the cBio Portal

  EGA cBioPortal What is the EGA cBioPortal? EGA hosts a dedicated cBioPortal instance that enables authorized researchers to explore and visualize selected cancer datasets archived at EGA. Data submitters can also contribute cancer datasets to be made available through the portal. The platform provides interactive tools to analyse genomic and clinical data once access has been granted by the relevant Data Access Committee (DAC). How to find and access an EGA cBioPortal Dataset 1. Register as an EGA user 2. Go to the dataset page of interest. You can use the Search function to find datasets available in cBioPortal. If the dataset is available on the EGA cBioPortal Instance, the cBioPortal icon will be displayed on the dataset page, as shown below: On the dataset page, you will find information about access requirements. For more details, please visit how to request access. 3. Once access has been granted Go to the EGA cBioPortal instance and log in with your EGA user accountThe approved dataset will be listed in cBioPortalSelect the dataset to start exploring the data What you can do in cBioPortal The EGA cBioPortal is designed for interactive exploration and visualization of controlled-access cancer datasets, including: Visualising genomic alterationsAnalysing mutation patternsFiltering by clinical attributesComparing molecular profilesGenerating plots and summaries Important Notes Datasets are only visible in cBioPortal after DAC approvalAccess requests must always be submitted through the EGA website If you encounter any issues gaining access to a dataset, please contact EGA Support.If your question is related to the cBioPortal features, please reach out to: cbioportal@googlegroups.com. The EGA Helpdesk does not support this platform. How to link a dataset to the EGA cBioPortal instance during a submission STEP 1 – cBioPortal File Upload to EGA Files must be uploaded to the SFTP INBOX. The supported cBioPortal file types are: Raw data (e.g., VCF files)cBioPortal-specific formats (e.g., MAF files) STEP 2 – Register the cBioPortal dataset in the Submitter Portal Register the cBioPortal files in an analysis objectRegister a dataset with the title “cBioPortal Metadata” and include the analysis and nothing else Please note that cBioPortal is not directly supported by the EGA Helpdesk. For questions about the platform, please visit the cBioPortal website or contact the cBioPortal support team at cbioportal@googlegroups.com. The EGA does not support this platform.

  Documentation submission/metadata/submission/cbioportal

• Low-coverage Whole Genome Sequencing, Colorectal adenomas, NKI-AvL TGO series Stool-Proteomics

  For this tissue dataset, we applied low-pass whole genome sequencing to 98 non-advanced and advanced adenomas. As small number of lesions was sequenced multiple times, this dataset consists of 103 fastq files. These adenomas were classified as lesions with low-risk or high-risk of progression, according to the presence of specific DNA copy number changes (Carvalho et al, CancerPrevRes, 2018).

  Dataset EGAD00001004075

• Omics data of advanced bladder cancer

  To identify the therapeutic targets in a treatment-refractory cancer patient, we performed single-cell RNA sequencing for 3,115 cells from primary bladder cancer (BC159-T#3) and patient-derived xenografts (BC159-T#3-PDX-vehicle and BC159-T#3-PDX-tipifarnib). Matched time-series bulk tumor tissues were also sequenced using whole exome target probe (WES) and whole transcriptome target probe (WTS).

  Dataset EGAD00001005978

• The Epigenomic Atlas of Early Human Craniofacial Development

  Parallel profiling of six distinct histone modifications via ChIP-Seq in craniofacial tissue samples from individual human embryos was performed. Epigenomic marks imputed with ChromImpute and a 25-state chromatin state model of uniformly processed epigenomic data was produced through ChromHMM. Samples were obtained from the MRC-Wellcome Trust Human Developmental Biology Resource (HDBR) tissue bank. HDBR provided karyotypically and developmentally normal pharyngeal arch or craniofacial tissue from embryos between 4.5 and 10 post-conception weeks. This repository contains raw data (fastq) files from ChIP-seq and RNA-seq experiments associated with this project. Processed ChIP-seq data and imputed data for additional histone marks are available at GEO (Series GSE97752).

  Study phs002008

• Improved Detection and Identification of Microsatellite Instability Features in Colorectal Cancer

  In this study, we analyzed a series of colorectal cancers using a new sequencing technology that sequences more than 200 microsatellite regions in parallel. With this technology, we evaluated mono-, di- , tri- and tetranucleotide repeats to provide a broad spectrum of microsatellite instability (MSI) events. This deep sequencing technology provides greater than 2000X coverage and eliminates the need for PCR amplification. Because every read corresponds to a single DNA molecule, we eliminated artifacts introduced by PCR that obscured true MSI events. Also included in our analysis is a new method for detection of somatic copy number changes in 83 cancer genes, with which we can infer chromosomal instability (CIN) status.

  Study phs001914

• Single-cell RNA sequence analysis of iPS cell-derived cardiomyocytes treated with S-RBD-sfGFP or GFP

  To determine the transcriptional response in human cardiomyocytes treated with SARS-CoV-2 spike receptor-binding domain (S-RBD-sfGFP), human cardiomyocytes differentiated from induced pluripotent stem cells (iPSC-CMs) were replated on day 21 after differentiation and treated with S-RBD-sfGFP or control-GFP for 48 hours on day 26-28. iPSC-CMs were dissociated and the single cell suspension was analyzed by single cell RNA-sequence.

  Study JGAS000620