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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, ATAC, 4 hr-1, rep1 (1st batch) |
| 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
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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 |
~1,500 cells were lysed followed by tagmentation using Tn5 transposase (Vazyme, TD502) following manufacturer’s protocols. The samples were then subjected to PCR amplification and purification for sequencing.
ATAC-seq libraries were prepared using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme) following manufacturer’s protocols.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Raw reads of ATAC-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.
Normalized reads count was calculated by Bedtools.
Assembly: mm10
Supplementary files format and content: bigWig, normalized reads count
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| Submission date |
Oct 03, 2023 |
| 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 |
SAMN37666426 |
| SRA |
SRX21980573 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7818710_EXOSC2_AID_ATAC_4hr1_rep1.bw |
85.1 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
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