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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jul 24, 2024 |
| Title |
K562, TET2 KO; siMBD6; siNC, ATAC, r2 |
| 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 KO, siMBD6
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| Treatment protocol |
siRNA transfections in leukemic cells were performed with SG Cell Line 4D-Nucleofector™ X Kit L (Lonza, V4XC-3024) or SF kit (V4XC-2012) using programs recommended by the manufacturer. siRNA transfections in mESCs were performed using Lipofectamine™ RNAiMAX Transfection Reagent (Invitrogen, 13778100) following the standard protocol. shRNA transfections in HSPCs were performed using electroporation. Gene overexpression in mESCs were performed by using the piggyBac transposase system with a hygromycin selection marker. Stable expression clones were selected by applying hygromycin B to the culture system for two weeks.
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| Growth protocol |
K-562 cells were kept in RPMI-1640 medium plus 10% FBS. 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 24 hours. mESCs were passaged on gelatin coated plates twice to clear feeder cells before experiments. HSPCs (lineage-positive cells (Lin+ ) were 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. HSPCs 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 for 7 days before assaying.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ATAC-seq was performed using a commercial kit (Active Motif, 53150) with ATAC-Seq Spike-In Control (Active Motif, 53154) following the standard protocol recommended by the manufacturer.
ATAC-seq was performed using a commercial kit (Active Motif, 53150) with ATAC-Seq Spike-In Control (Active Motif, 53154) following the standard protocol recommended by the manufacturer.
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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) or human genome (hg38), together with Drosophila melanogaster chromatin (Spike-in Chromatin), using bowtie2 (version 2.4.1) with default mode, where multiple alignments are searched and the best one is reported.
Mapped reads were deduplicated using a Picard tool ‘MarkDuplicates’ (version 2.26.2) (http://broadinstitute.github.io/picard/). Reads that mapped to the mitochondrial genome were discarded prior to deduplication.
Peaks were identified using MACS266 with the default mode, except for the parameters “--shift -75 --extsize 150 --nomodel --call-summits”.
Assembly: mm10 (mouse), hg38 (human)
Supplementary files format and content: Peaks
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| Submission date |
Jun 15, 2024 |
| 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) |
| GSE241347 |
Chromatin-associated LTR RNA m5C oxidation by TET2 regulates leukemogenesis |
| GSE269958 |
Chromatin-associated LTR RNA m5C oxidation by TET2 regulates chromatin state and leukemogenesis [seq_DNA-ATAC_set2] |
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| Relations |
| BioSample |
SAMN41851450 |
| SRA |
SRX24937249 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8331448_K562_TET2KO-siMBD6_ATAC_r2_peaks.narrowPeak.gz |
3.1 Mb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
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