{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Dawn Lin"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-17343"],"description":["Low-input bulk ATAC-seq of EPCR+ and EPCR– subsets of HSC and MPP1-6 populations was performed to compared the chromatin accessibility differences between these cell types."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - cells were sorted, pelleted and resuspended in cold lysis buffer, followed by incubation on ice for three minutes to release nuclei. Nuclei were then washed in ATAC-Resuspension Buffer (RSB) containing 0.1% Tween-20, pelleted, and resuspended in transposition buffer containing Tn5 transposase. Transposition reactions were performed via incubation at 37 °C in a thermomixer with shaking at 1,000 rpm for 30 minutes.","Sequencing - Following a final bead cleanup, libraries were pooled to 10 nM and sequenced on an Illumina NovaSeq 6000 platform to generate paired-end 100 bp reads.","Library Construction - DNA was purified using AMPure XP magnetic beads and libraries were amplified by qPCR using NEBNext High-Fidelity Master Mix and custom i5 and i7 primers.","Sample Collection - To prepare for BM cell suspension, bones were crushed and incubated with ACK buffer for 5 minutes at room temperature to remove excess red blood cells. Lineage depletion was performed using the EasySep Mouse Hematopoietic Progenitor Cell Isolation Kit (STEMCELL technologies, #19856) according to the manufacturer’s instruction. The Lin-depleted cells were then stained with the following antibodies: BV711 anti-mouse c-Kit (clone 2B8; BioLegend; 105835) or BUV395 anti-mouse c-Kit (clone 2B8; BD Biosciences; 564011), APC-Cy7 anti-mouse Sca1 (clone D7; BD Biosciences; 560654), PE anti-mouse EPCR (clone eBio1560; eBioscience; 12-2012-82), FITC anti-mouse CD34 (clone RAM34; eBioscience; 11-0341-82) or eFluor 660 anti-mouse CD34 (clone RAM34; eBioscience; 50-0341-82), PE-Cy7 an"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Data preprocessing was performed using the Nextflow nf-core/atacseq pipeline with the narrow peak option and min_resp_consensus=2 in MACS2-based peak calling and default parameters otherwise. Sample quality was assessed using the fraction of reads in called peak regions (FRiP) score as obtained from the nf-core/atacseq pipeline. All samples with a FRiP score > 0.2 were considered to be of high quality and used for downstream analysis. For conditions, in which the high-quality replicate number was < 3, additional samples ranked by decreasing FRiP score were added to reach a total of 3 given that the FRiP score exceeded the minimum threshold of 0.08. As there was only a single replicate for MPP4* EPCR-negative, this condition was excluded from the analysis.  Peaks with "],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NA","Flow Cytometer","Real-time PCR Thermal Cycler","Illumina NovaSeq 6000","Thermomixer"],"study_type":["ATAC-seq"],"species":["Mus musculus"],"pubmed_authors":["Dawn Lin"],"additional_accession":[]},"is_claimable":false,"name":"Low-input ATAC-seq of mouse EPCR+ and EPCR– hematopoietic stem cell and multipotent progenitor cell populations","description":"Low-input bulk ATAC-seq of EPCR+ and EPCR– subsets of HSC and MPP1-6 populations was performed to compared the chromatin accessibility differences between these cell types.","dates":{"release":"2026-07-18T00:00:00Z","modification":"2026-07-18T01:01:04.047Z","creation":"2026-07-10T15:50:31.639Z"},"accession":"E-MTAB-17343","cross_references":{"ENA":["ERP201052"],"EFO":["EFO_0002944","EFO_0007045","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0004184"]}}