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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 16, 2024 |
| Title |
EXOSC2 AID ESCs, S2P Pol II, spikein, 4 hr rep1 |
| Sample type |
SRA |
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| Source name |
AID-FBEXOSC2 ESCs
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| Organism |
Mus musculus |
| Characteristics |
cell line: AID-FBEXOSC2 ESCs
cell type: mouse embryonic stem cell
treatment: IAA
time: 4 hour
chip antibody: Ser2P Pol II (CST, Cat#: 13499)
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| Treatment protocol |
EXOSC2 degradation was induced by treatment of IAA (0.5 mM, Sigma, Cat#: I5148) for indicated hours to adherent ESCs.
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| Growth protocol |
AID-FBEXOSC2 ESCs were maintained in a complete ESC culture medium that consisted of DMEM (Corning) supplemented with 15% heat-inactivated fetal bovine serum (FBS), GlutaMAX (100× stock, Gibco), Penicillin-Streptomycin Solution (100× stock, Corning), MEM nonessential amino acids (100× stock, Gibco), nucleoside mix (100× stock, Millipore), 0.1 mM 2-mercaptoethanol (Gibco), and supplied with 1000 U/ml recombinant leukemia inhibitory factor (LIF, Millipore). The mESCs were seeded onto 0.1% gelatin-coated dishes. All cultured cells were maintained in a humidified incubator at 37°C with 5% CO2.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated and subjected to immunoprecipitation. After elution and reverse-crosslinking, the DNA was purified using DNA Clean-up Kit (CWBIO). We added cross-linked 293T cells as spike-in to cross-linked AID-FBEXOSC2 ESCs and then performed cell lysis and all downstream procedures to indicate cell number.
ChIP-seq libraries were prepared using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme) following manufacturer’s protocols.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Raw reads of ChIP-seq were mapped to mouse genome mm10 by Bowtie2 (version 2.2.6). All unmapped reads, non-uniquely mapped reads and PCR duplicates were removed. For Pol II ChIP-seq with 293T spike-in, we additionally mapped the raw reads to human genome hg19, which is DNA spike-in, and normalized to spike-in reads.
Normalized reads count was calculated by Bedtools.
Assembly: mm10
Supplementary files format and content: bigWig, cell number normalized reads count
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| Submission date |
Feb 12, 2024 |
| Last update date |
Apr 16, 2024 |
| Contact name |
Xue Han |
| E-mail(s) |
xuehan89@126.com
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| Organization name |
Tsinghua University
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| Department |
School of Medicine
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| Lab |
Shen Xiaohua Lab
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| Street address |
Zhongguancun North Street
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| City |
Beijing |
| ZIP/Postal code |
100084 |
| Country |
China |
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| Platform ID |
GPL21273 |
| Series (1) |
| GSE237465 |
Nuclear RNA homeostasis promotes systems-level coordination of cell fate and senescence |
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| Relations |
| BioSample |
SAMN39925928 |
| SRA |
SRX23607145 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8076036_EXOSC2_AID_S2PPolII_spikein_4hr_rep1.bw |
110.4 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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