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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, RNA, np, rep1, 0 hr |
| 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 |
Cells were fractionated by sequential lysis and centrifugation. We first isolated the cytosolic fraction (‘cyto’) by 0.15% NP-40, and then used salt and detergents (0.15 M NaCl, 0.5 M urea and 0.5% NP40) to partition nuclear constituents. The soluble nucleoplasmic fraction (‘np’) with greater biochemical extraction captured the highly dynamic RNP mesh components, whereas the insoluble fraction contained chromatin and less extractable RNP mesh components, designated as the ‘chr/RNPmesh’. Add the RNA spike-in (a combination of GFP, mCherry, lacZ, and Luciferase transcripts) directly to the samples of each subcellular fraction according to number of cells for normalization. Total RNA were extracted by TRIzol reagent according to manufacturer's instruction. Purified total RNA were subjected to ribosomal RNA depletion by Ribo-Zero rRNA removal kits (Illumina) according to manufacturer's instruction.
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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 |
Raw reads of RNA-seq were mapped to mouse genome mm10 by TopHat (version 2.0.11). We additionally mapped the raw reads to an in-house reference containing spike-in sequence (GFP, mCherry, lacZ and Luciferase).
FPKM was calculated by Cufflinks (version 2.0.2) using 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 FPKM values for RNA-seq samples
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| Submission date |
Sep 25, 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 |
SAMN37538230 |
| SRA |
SRX21883914 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7804818_EXOSC2_AID_np_0hr_rep1_fwd.bw |
62.6 Mb |
(ftp)(http) |
BW |
| GSM7804818_EXOSC2_AID_np_0hr_rep1_rev.bw |
60.1 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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