Basic Information
| Dataset | GSE192376 |
|---|---|
| Status | 2022-05-18 |
| Species | Homo sapiens |
| Source | NCBI GEO |
| Subcellular Localization | nuclear|cytosolic |
| PMID | 35589130 |
| Title | RNA-fractionation sequencing |
| Citation | Thomas A, Rehfeld F, Zhang H, Chang TC et al. RBM33 directs the nuclear export of transcripts containing GC-rich elements. Genes Dev 2022 May 1;36(9-10):550-565. |
| Experimental Design | 400 000 WT, RBM33 KO-1, or RBM33 KO-2 HCT116 cells were seeded in 6-well plates. For each replicate, 48 hours later, one well was subjected to total RNA extraction and one well to nuclear-cytoplasmic fractionationFractionation was performed as described previously (Lee et al., 2016). Briefly, cells were collected by trypsinization and lysed in 175 µL RLN1 buffer [50 mM Tris-HCl pH 8, 140 mM NaCl, 1.5 mM MgCl2, 0.5% NP-40, and 1:1000 SUPERase In RNase inhibitor (Thermo Fisher Scientific)]. Following a 5-minute incubation on ice, the sample was centrifuged at 300 g for 2 minutes. The supernatant, representing the cytoplasmic fraction, was collected and centrifuged at 16000 g for 5 minutes to clear debris. The initial pellet, representing the nuclear fraction, was gently resuspended in 500 µL RLN1 and centrifuged at 1000 g for 5 minutes to wash. The pellet was then resuspended in 175 µL RLN2 buffer [50 mM Tris-HCl pH 8, 500 mM NaCl, 1.5 mM MgCl2, 0.5% NP-40, and 1:1000 SUPERase In RNase inhibitor (Thermo Fisher Scientific)]. RNA was extracted from each of these fractions by Trizol in combination with the miRNeasy mini kit (Qiagen) with an on-column DNase digestion. |
Sample Information
| BioProject | Sample Name | Localization | Genotype | Source | Label |
|---|---|---|---|---|---|
| PRJNA791311 | GSM5745792 | cytosolic RNA fraction | RBM33 KO clone1 | HCT116 colon cancer cell line | RBM33 KO clone1 replicate 1 cytosolic fraction |
| PRJNA791311 | GSM5745793 | nuclear RNA fraction | RBM33 KO clone1 | HCT116 colon cancer cell line | RBM33 KO clone1 replicate 1 nuclear fraction |
| PRJNA791311 | GSM5745794 | total RNA | RBM33 KO clone1 | HCT116 colon cancer cell line | RBM33 KO clone1 replicate 1 total |
| PRJNA791311 | GSM5745795 | cytosolic RNA fraction | RBM33 KO clone1 | HCT116 colon cancer cell line | RBM33 KO clone1 replicate 2 cytosolic fraction |
| PRJNA791311 | GSM5745796 | nuclear RNA fraction | RBM33 KO clone1 | HCT116 colon cancer cell line | RBM33 KO clone1 replicate 2 nuclear fraction |
| PRJNA791311 | GSM5745797 | total RNA | RBM33 KO clone1 | HCT116 colon cancer cell line | RBM33 KO clone1 replicate 2 total |
| PRJNA791311 | GSM5745798 | cytosolic RNA fraction | RBM33 KO clone2 | HCT116 colon cancer cell line | RBM33 KO clone2 replicate 1 cytosolic fraction |
| PRJNA791311 | GSM5745799 | nuclear RNA fraction | RBM33 KO clone2 | HCT116 colon cancer cell line | RBM33 KO clone2 replicate 1 nuclear fraction |
| PRJNA791311 | GSM5745800 | total RNA | RBM33 KO clone2 | HCT116 colon cancer cell line | RBM33 KO clone2 replicate 1 total |
| PRJNA791311 | GSM5745801 | cytosolic RNA fraction | RBM33 KO clone2 | HCT116 colon cancer cell line | RBM33 KO clone2 replicate 2 cytosolic fraction |
| PRJNA791311 | GSM5745802 | nuclear RNA fraction | RBM33 KO clone2 | HCT116 colon cancer cell line | RBM33 KO clone2 replicate 2 nuclear fraction |
| PRJNA791311 | GSM5745803 | total RNA | RBM33 KO clone2 | HCT116 colon cancer cell line | RBM33 KO clone2 replicate 2 total |
| PRJNA791311 | GSM5745804 | cytosolic RNA fraction | WT | HCT116 colon cancer cell line | WT replicate 1 cytosolic fraction |
| PRJNA791311 | GSM5745805 | nuclear RNA fraction | WT | HCT116 colon cancer cell line | WT replicate 1 nuclear fraction |
| PRJNA791311 | GSM5745806 | total RNA | WT | HCT116 colon cancer cell line | WT replicate 1 total |
| PRJNA791311 | GSM5745807 | cytosolic RNA fraction | WT | HCT116 colon cancer cell line | WT replicate 2 cytosolic fraction |
| PRJNA791311 | GSM5745808 | nuclear RNA fraction | WT | HCT116 colon cancer cell line | WT replicate 2 nuclear fraction |
| PRJNA791311 | GSM5745809 | total RNA | WT | HCT116 colon cancer cell line | WT replicate 2 total |
| PRJNA791311 | GSM5745810 | cytosolic RNA fraction | WT | HCT116 colon cancer cell line | WT replicate 3 cytosolic fraction |
| PRJNA791311 | GSM5745811 | nuclear RNA fraction | WT | HCT116 colon cancer cell line | WT replicate 3 nuclear fraction |
| PRJNA791311 | GSM5745812 | total RNA | WT | HCT116 colon cancer cell line | WT replicate 3 total |
Subcellular Localization Number
RNA Type:
Condition:
Localization Differential Analysis
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Method:
Enrichment:
Specific Subcellular Localization
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Method:
Dynamic RNA Localization
RNA Type:
Method:
Specific Enrichment Analysis
RNA Type:
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Condition:
Method:
Enrichment:
Specific RNA Ratio
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TPM:
