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| Status |
Public on Jul 24, 2024 |
| Title |
K562, TET2 KO, H2AK119ub, CUT&Tag, rep1 |
| Sample type |
SRA |
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| Source name |
bone marrow
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| Organism |
Homo sapiens |
| Characteristics |
tissue: bone marrow
cell line: K562
cell type: lymphoblast cell
genotype: TET2 knockout
antibody: H2AK119ub (CST, #8240S)
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| Treatment protocol |
siRNA transfections in K-562 was performed according to the standard protocols of Lonza Walkersville SF Cell Line 4D-Nucleofector X Kit L (Lonza, V4XC2024) with program FF-120.
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| Growth protocol |
K-562 cell lines were kept in RPMI-1640 (Gibco, 61870036) with 10% fetal bovine serum (FBS, Gibco) and 1 μg/mL puromycin (Gibco, A1113803) at 37 °C and 5% CO2. 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 |
N/A
CUT&Tag libraries were constructed following the manufacturer's instructions of CUT&Tag-IT™ Assay Kit (Active Motif, 53160).
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| Library strategy |
OTHER |
| 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) or human genome (hg38) using bowtie2 (version 2.4.1) with default mode, where multiple alignments are searched and the best one is reported.
Peaks were called using HOMER (version 4.9) in histone mode with reads deduplicated by using ‘-tbp 1’ parameter.
Assembly: mm10 for mouse and hg38 for human
Supplementary files format and content: Peaks
Library strategy: CUT&Tag
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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 |
GPL24676 |
| Series (2) |
| GSE241304 |
TET2 regulates histone H2AK119ub and leukemogenesis through LTR RNA m5C oxidation [seq_DNA-CUTandTag] |
| GSE241347 |
Chromatin-associated LTR RNA m5C oxidation by TET2 regulates leukemogenesis |
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| Relations |
| BioSample |
SAMN37094980 |
| SRA |
SRX21436097 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7720848_K562_TET2-KO_H2AK119ub_CUTandTag_rep1_peaks.bed.gz |
1.1 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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