{"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-15477"],"description":["Single cell Methylome and Transcriptome Sequencing (scM&T-Seq) was performed on index-sorted single CD48- CD135- Lin- Sca-1+ c-Kit+ cells from Scl-tTA; H2B-GFP mouse bone marrow after 100 days of chase.  Methylation data is uploaded here."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - Single-cell methylome and transcriptome sequencing (scM&T-seq) libraries were generated based on the high-throughput protocol published previously (Cerrizuela et al., 2022) with the modification that no GpC methyltransferase incubation was done and that 384 cell could be multiplexed for the sequencing of the methylation layer.","Sample Collection - Scl-tTA; H2B-GFP mice were treated with doxycycline for 100 days, which turn off constitutively expressed H2B-GFP, thus allow the marking of H2B-GFP+ dormant cells and H2B-GFP- active cell. Bone marrow was isolated after 100 days of chase, red cell lysed and lineage depleted 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), APC-Cy7 anti-mouse Sca1 (clone D7; BD Biosciences; 560654), PE anti-mouse EPCR (clone eBio1560; eBioscience; 12-2012-82), 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), 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). Index sorting was performed to sort single CD48– CD135- LSK cells into 384-well plate containing 2 µL RLP plus buffer (Qiagen, Cat #1053393) and 1 µL water per well and immediately frozen at -80 °C.","Sequencing - gDNA was sequenced on a NextSeq2000 P3 (100bp PE).","Nucleic Acid Extraction - single cells were lysed in 2 µL RLP plus buffer (Qiagen, Cat #1053393) and 1 µL water per well and immediately frozen at -80 °C."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Genomic reads were trimmed and adapters were removed with TrimGalore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) in paired end mode. They were then mapped to GRCm39 using Bismark 0.22.3 in non-directional, single end mode. Each .bam file of the two pairs was deduplicated with Bismark’s `deduplicate_bismark` and then merged with `samtools merge`. DNA methylation calls at CpGs were obtained using Bismark’s `methylation_extractor`. CpG DNA methylation for the scM&T-seq plate was analyzed using MethScan 1.1.0 to quantify methylation in variably methylated regions (VMRs). Cells with CpG coverage defined in less than 60000 sites were excluded from further analysis. To visually inspect the quality of single cell methylomes, methylation values were profiled in a curated set of TSS sites (as defined in Kremer et al.,) using `methscan profile`. After filtering, methylation values were smoothed with `methscan smooth` using a window of 100bp. VMRs were called with `methscan scan` using a bandwidth of 2000bp for the sliding window, a stepsize of 100bp, and a variance threshold of 0.02 to select the top 2% most variable genomic bins. The final cell-by-VMR matrix was generated using `methscan matrix`, where DNA methylation levels for each region were quantified as a shrunken mean of residuals."],"omics_type":["Unknown","Transcriptomics","Genomics"],"instrument_platform":["Flow cytometer","NextSeq 2000"],"study_type":["methylation profiling by high throughput sequencing"],"species":["Mus musculus"],"pubmed_authors":["Dawn Lin"],"additional_accession":[]},"is_claimable":false,"name":"Single cell methylation of dormant and active hematopoietic stem cell and multipotent progenitor from H2B-GFP bone marrow after 100 days of chase","description":"Single cell Methylome and Transcriptome Sequencing (scM&T-Seq) was performed on index-sorted single CD48- CD135- Lin- Sca-1+ c-Kit+ cells from Scl-tTA; H2B-GFP mouse bone marrow after 100 days of chase.  Methylation data is uploaded here.","dates":{"release":"2025-08-06T00:00:00Z","modification":"2025-08-12T21:19:02.915Z","creation":"2025-08-12T21:19:02.915Z"},"accession":"E-MTAB-15477","cross_references":{"ENA":["ERP178701"],"EFO":["EFO_0002944","EFO_0004170","EFO_0002761","EFO_0005518","EFO_0003816","EFO_0004184"]}}