{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Lina Antounians"],"instrument_platform":["Illumina HiSeq 2500"],"study_type":["ChIP-seq"],"organism":["Rattus norvegicus"],"species":["Rattus norvegicus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14612"],"description":["This accession ID containes ChIP-seq data for JUN, H3K27ac, H3K4me3 and H3K4me2 in primary aortic endothelial cells. This data will be used for:  1) A phylogenetic framework for comparative analysis of chromatin state in mammalian species. Sara Knaack, Lina Antounians, Azad Alizada, Alejandra Medina-Rivera, Michael D. Wilson, and Sushmita Roy  2) Inter-tissue, interspecies comparisons of JUN occupancy in vascular endothelial cells identify regulatory mechanisms associated with vascular disease. Alejandra Medina-Rivera, Lina Antounians, Marisol Alvarez-Martinez, Azad Alizada, Michael Liang, Liis Uusküla-Reimand,France Gagnon, Jason Fish, Michael D. Wilson"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - Samples were submitted for quality control analysis to the Donnelley Sequencing Center (University of Toronto) for Bioanalyzer analysis and library quantification using KAPA Biosystems. Libraries were sequenced using Illumina HiSeq2500. The flowcells were prepared and processed by the sequencing facility according to the manufacturer's protocol, with 100-bp single-end sequencing for 75 cycles.","Growth Protocol - EC were grown in supplier-recommended Endothelial Cell Growth Media (Cell Applications, catalogue #211-500) and cultured at 37° C in a 5%-CO2 humidified incubator.","Sample Collection - Chromatin immunoprecipitation experiments were conducted as previously described in (Schmidt et al. 2009). Antibodies used for ChIP were mouse anti-H3K27ac (Millipore, 05-1334 monoclonal)and rabbit anti-Jun (Santa Cruz Biotechnology, sc1694 polyclonal).","Library Construction - ChIP DNA was prepared for Illumina sequencing by blunt-end repair, dA-tailing, and ligation of Illumina adaptors using a NEBNext DNA library preparation kit (New England Biolabs, catalogue #E6040L). Total ChIP DNA (approximately 200-500ng) and 220ng of DNA input (WCE) was end repaired for 30 minutes at room temperature, and then purified using column purification with either DNA Clean and Concentrator (Zymogen, catalogue #D4014) or PCR purification columns (Qiagen, catalogue #28106) as recommended by manufacturer’s protocol. Blunt-end repaired DNA was dA-tailed for 40 minutes at 37° C, then column purified. dA-tailed DNA was ligated to Illumina adaptors (final concentration 6.67 nM). USER enzyme was used to cleave the uracil hairpin of the Illumina adaptor, and adaptor-ligated DNA was column purified. The library was PCR amplified for 16-18 cycles using a universal primer and a barcoded primer (New England Biolabs, catalogue #E7335L). PCR-amplified DNA was purified using PCR column purification and eluted in 20 uL of elution buffer for preparation of gel extraction, or 30 uL of TE for preparation of Pippin Prep size selection. Libraries were size selected from 200-350bp using a 2% agarose gel or a dye-free automated size selection cassette from Pippin Prep (Sage Sciences, catalogue #CDF2010).","Growth Protocol - EC were grown in Endothelial Cell Medium (ScienCell, catalogue #1001)"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"pubmed_authors":["Lina Antounians","Alejandra Medina-Rivera","Michael Wilson"],"additional_accession":[]},"is_claimable":false,"name":"Comparative epigenomic analysis of JUN, H3K27ac, H3K4me3 and H3K4me2 in primary aortic endothelial cells","description":"This accession ID containes ChIP-seq data for JUN, H3K27ac, H3K4me3 and H3K4me2 in primary aortic endothelial cells. This data will be used for:  1) A phylogenetic framework for comparative analysis of chromatin state in mammalian species. Sara Knaack, Lina Antounians, Azad Alizada, Alejandra Medina-Rivera, Michael D. Wilson, and Sushmita Roy  2) Inter-tissue, interspecies comparisons of JUN occupancy in vascular endothelial cells identify regulatory mechanisms associated with vascular disease. Alejandra Medina-Rivera, Lina Antounians, Marisol Alvarez-Martinez, Azad Alizada, Michael Liang, Liis Uusküla-Reimand,France Gagnon, Jason Fish, Michael D. Wilson","dates":{"release":"2025-06-19T00:00:00Z","modification":"2024-11-18T17:29:25.74Z","creation":"2024-11-18T17:29:25.74Z"},"accession":"E-MTAB-14612","cross_references":{"ENA":["ERP166309"],"EFO":["EFO_0004170","EFO_0003789","EFO_0002692","EFO_0005518","EFO_0004184"]}}