{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Jan-Inge Bjune"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-13540"],"description":["A map of open chromatin in primary preadipocytes isolated from male and female mouse gWAT and iWAT on days -1, 0, 4h, 1, 2, 7 and mature stage of adipogenic differentiation.  On indicated days, cells were permeabilized and nuclei released. Tagmentation was performed according to Buenrostro et al. 2015. Tagmented DNA was amplified by PCR and the libraries assessed on a Bioanalyzer, followed by 75 bp paired end sequencing on an Illumina HiSeq4000 platform."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - Transposition reaction was performed as previously described (Buenrostro et al. 2015). All tagmented DNA was PCR amplified for 11-13 cycles. Quality was assessed using a DNA1000 Chip (Applied Biosystems) and run on a Bioanalyzer (Applied Biosystems). The profiles showed that all libraries had a mean fragment size of ~190 bp and characteristic nucleosome patterning, indicating good quality of the libraries.","Nucleic Acid Extraction - Lysis buffer was gently pipetted up and down to wash nuclei off the well and transferred into a chilled 1.5ml tube to create crude nuclei. Nuclei were spun down at 600 x g for 10 min at 4℃, nuclei pellets were then re-suspended in 40 µl Tagmentation DNA (TD) Buffer.","Sample Collection - Mouse inguinal and gonadal white adipose tissues where excised from 6-10 weeks old C57BL/6NJ (B6N) mice fed ad libitum with SDS maintenance chow (RM3, 3.6 kcal/g).Primary preadipocytes were isolated from the WAT depots by by collagenase digestion and centrifugation to separate floating adipocytes from the SVF pellet. The SVF was resuspended in DMEM GlutaMax culture medium supplemented with 10% FBS and 1% PEST. The cell suspension was filtered through a 40 um mesh and pooled cells from 6-12 mice were seeded on a 10 cm dish at a density of 100.000 cells/mL.Cells were grown to confluence, and induced to differentiate 2 days post confluency by addition of 0.5 mM IBMX, 1 uM Dex, 5 ug/mL human Insulin to the growth media. On days -1, 0, 0,4h, 1, 2, 7 and mature stage, cells lysed directly in the cell culture plate and nuclei released.","Sequencing - Libraries were sequenced at the Wellcome Trust Centre for Human Genetics in Oxford on a HiSeq4000 Illumina generating 50 million reads/sample, 75bp paired end. To reduce bias due to PCR amplification of libraries, duplicate reads were removed."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Reads were first filtered for mapping quality ≥ 30 (samtools Version 1.7-2) and duplicated reads, as well as reads mapping to the mitochondria, were subsequently removed (picardTools Version 2.8.1.1). Peak calling was performed via Macs2 (Version 2.1.1). Peak sets were first filtered using blacklisted regions from the ENCODE project [91], then converted into a simple annotation format for submission to the Rsubread featureCounts (Version 1.6.0) package. Using this consensus peak set as an annotation guide, each unmerged bam file was submitted to featureCounts and the subsequent count matrix was input into RStudio for peak annotation and visualization."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NA","Illumina HiSeq 4000"],"study_type":["ATAC-seq"],"species":["Mus musculus"],"pubmed_authors":["Jan-Inge Bjune"],"additional_accession":[]},"is_claimable":false,"name":"ATAC seq of isolated primary preadipocytes from male and female mouse gWAT and iWAT on multiple days of differentiation","description":"A map of open chromatin in primary preadipocytes isolated from male and female mouse gWAT and iWAT on days -1, 0, 4h, 1, 2, 7 and mature stage of adipogenic differentiation.  On indicated days, cells were permeabilized and nuclei released. Tagmentation was performed according to Buenrostro et al. 2015. Tagmented DNA was amplified by PCR and the libraries assessed on a Bioanalyzer, followed by 75 bp paired end sequencing on an Illumina HiSeq4000 platform.","dates":{"release":"2025-05-16T00:00:00Z","modification":"2024-11-26T12:01:30.389Z","creation":"2023-11-17T12:26:50.002Z"},"accession":"E-MTAB-13540","cross_references":{"ENA":["ERP154631"],"EFO":["EFO_0002944","EFO_0007045","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0004184"]}}