biostudies-arrayexpressDawn LinMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-17343Low-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.biostudies-arrayexpressNucleic 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.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 anti-mouse CD48 (clone HM48-1; BioLegend; 103424), BV421 anti-mouse CD135 (clone A2F10.1; BD Biosciences; 562898) or APC anti-mouse CD135 (clone A2F10; BioLegend; 135310),PE-Cy5 anti-mouse CD150 (clone TC15-12F12.2; BioLegend; 115912) or BV785 anti-mouse CD150 (clone TC15-12F12.2; BioLegend; 115937), BUV496 anti-mouse CD16/32 (clone Ab93; BD Biosciences; 751694), Alexa Fluor 700 anti-mouse CD4 (clone GK1.5; eBioscience; 56-0041-82),Alexa Fluor 700 anti-mouse CD8a (clone 53-6.7; eBioscience; 56-0081-82), Alexa Fluor 700 anti-mouse CD11b (clone M1/70; eBioscience; 56-0112-82),Alexa Fluor 700 anti-mouse GR1 (clone RB6-8C5; eBioscience; 56-5931-82), Alexa Fluor 700 anti-mouse B220 (clone RA3-6B2; eBioscience; 56-0452-82), Alexa Fluor 700 anti-mouse Ter119 (clone TER-119; BioLegend; 116220). All antibody staining were performed at 4 °C for approximate 30 minutes. Cells were then washed to remove unbound antibodies and resuspended in FACS buffer containing 7-AAD (BD Biosciences; 51-68981E) prior to cell sorting using BD FACSAria-II/III, BD Fusion or BD Symphony S6 (BD Biosciences). Between 300 – 3000 cells from each HSPC populations were sorted.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.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData 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 a minimum count of 10 in at least three samples were included in the analysis. To obtain normalized counts, a DESeq2 model was fit based on the identity of the biological populations for all but EPCR- and CD150-based comparisons and is provided here as rds object.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsNAFlow CytometerReal-time PCR Thermal CyclerIllumina NovaSeq 6000ThermomixerATAC-seqMus musculusDawn LinfalseLow-input ATAC-seq of mouse EPCR+ and EPCR– hematopoietic stem cell and multipotent progenitor cell populationsLow-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.2026-07-18T00:00:00Z2026-07-18T01:01:04.047Z2026-07-10T15:50:31.639ZE-MTAB-17343ERP201052EFO_0002944EFO_0007045EFO_0004170EFO_0005518EFO_0003816EFO_0004184