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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, nascent RNA, EU, 0 hr, rep2 |
| 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: none
time: 0 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 |
total RNA |
| Extraction protocol |
ESCs were labeled with 1 mM 5-EU for 10 minutes and harvested by TRIzol with the addition of RNA spike-ins (5-EU labeled S2 cells) for cell number control. Apply purified RNA to DNase I treatment, fragmentation, ethanol precipitation, and biotinylation. Purify biotinylated RNA by phenol-chloroform, followed by two rounds of biotin-affinity purification using M-280 Streptavidin Dynabeads.
Eluted RNA was applied for cDNA synthesis and strand-specific library construction by ssDNA-seq Lib Prep Kit (Abclonal, Cat#: RK20222) following manufacturer’s protocols.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Adapters and low-quality reads were removed and polyC tracts were cut from the reads by Trim_galore. Reads of RNA-seq were mapped to mouse genome mm10 by TopHat (version 2.0.11). We additionally mapped the raw reads to drosophila genome dm6, which is the RNA spike-in.
RPKM was calculated for each genebody from Gencode vM16 annotation with redundant genes removed (a list containing 52,885 annotated genes).
Normalized reads count was calculated by Bedtools.
Assembly: mm10
Supplementary files format and content: bigWig, cell number normalized reads count
Supplementary files format and content: tab-delimited text file includes RPKM values for RNA-seq samples
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| Submission date |
Sep 29, 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 |
SAMN37607884 |
| SRA |
SRX21932232 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7813943_EXOSC2_AID_nascentRNA_EU_0hr_rep2_fwd.bw |
9.3 Mb |
(ftp)(http) |
BW |
| GSM7813943_EXOSC2_AID_nascentRNA_EU_0hr_rep2_rev.bw |
8.8 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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