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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jul 24, 2024 |
| Title |
mESC, Pspc1 WT, ATAC, rep2 |
| Sample type |
SRA |
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| Source name |
embryos
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| Organism |
Mus musculus |
| Characteristics |
tissue: embryos
cell line: mESC
cell type: mouse embronic stem cell
genotype: wildtype
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| Growth protocol |
For hematopoietic stem and progenitor Lin-c-Kit+ (LK) cell selection, magnetic-activated cell sorting was applied with autoMACS® Pro Separator (Miltenyi Biotec). Briefly, the lineage-positive cells (Lin+) were firstly depleted from total BM cells of 6–8 weeks old mice using the Direct Lineage Cell Depletion Kit (Miltenyi Biotec, 130-110-470), and then the lineage-negative cells (Lin-) were sorted with c-Kit (CD117) MicroBeads (Miltenyi Biotec, 130-091-224). The purity of selected cells was analyzed by flow cytometry. The LK cells were also incubated in suspension culture containing 30% FBS and 2% BSA in complete RPMI-1640 medium supplemented with 100 ng/mL mSCF, 10 ng/mL mIL-3, 50 ng/mL mTPO and 10 ng/ml mGM-CSF. All mESCs were kept in DMEM (Gibco, 11995065) supplemented with 15% Stem Cell Qualified Fetal Bovine Serum, Heat Inactivated (Gemini Bio Products, 100-525), 1 × L-glutamine (Gibco, 25030081), NEAA (Gibco, 25030081), LIF (MilliporeSigma, ESG1107), 1 × β-mercaptoethanol (Gibco, 21985023), 3 μM CHIR99021 (STEMCELL Technologies, 72052) and 1 μM PD0325901 (STEMCELL Technologies, 72182) at 37 °C and 5% CO2. The medium was replaced every day. ES cells were passaged on gelatin-coated plates twice to clear feeder cells before experiments.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
NGS libraries were obtained directly from cultured cells. Library constructions were conducted by following the manufacturer's instructions for ATAC-Seq Kit (Active Motif, 53150).
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Raw reads were trimmed with Trimmomatic (version 0.39) and then mapped to mouse genome (mm10) using bowtie2 (version 2.4.1) with default mode, where multiple alignments are searched and the best one is reported.
Reads mapped to the mitochondrial genome were discard and then the remaining reads were deduplicated using a Picard tool ‘MarkDuplicates’ (version 2.26.2) (http://broadinstitute.github.io/picard/).
Assembly: mm10
Supplementary files format and content: bigWig
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| Submission date |
Aug 21, 2023 |
| Last update date |
Jul 24, 2024 |
| Contact name |
Xiaoyang Dou |
| E-mail(s) |
xiaoyang.dou@sibcb.ac.cn
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| Organization name |
Center for Excellence in Molecular Cell Science, CAS
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| Street address |
320 Yue Yang Road
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| City |
Shanghai |
| ZIP/Postal code |
200031 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE241299 |
TET2 regulates histone H2AK119ub and leukemogenesis through LTR RNA m5C oxidation [seq_DNA-ATAC] |
| GSE241347 |
Chromatin-associated LTR RNA m5C oxidation by TET2 regulates leukemogenesis |
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| Relations |
| BioSample |
SAMN37095216 |
| SRA |
SRX21436142 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7720793_mESC_Pspc1-WT_ATAC_rep2.bigWig |
318.3 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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