Basic Information
| Dataset | GSE206328 |
|---|---|
| Status | 2023-12-22 |
| Species | Homo sapiens |
| Source | NCBI GEO |
| Subcellular Localization | nucleus|cytoplasm|PE (pellet extract)|CBNE (chromatin-bound nuclear extract)|SNE (soluble nuclear extract)|ME (membrane extract)|CE (cytoplasmic extract) |
| PMID | 38134924 |
| Title | Atlas of subcellular RNA localization in human embryonic stem cells and its flow during differentiation |
| Citation | Zhou F, Tan P, Liu S, Chang L et al. Subcellular RNA distribution and its change during human embryonic stem cell differentiation. Stem Cell Reports 2024 Jan 9;19(1):126-140. |
| Experimental Design | Operations refer to Subcellular Protein Fractionation Kit’s (Thermo Fisher, 78840) instruction. We collected cells and added cytoplasmic extraction buffer in the tube. After incubating the tube at 4°C for 10 min and centrifuging at 500 × g for 5 min, we immediately transferred the supernatant (cytoplasmic extract). Then we added the membrane extraction buffer, incubated at 4℃ for 10 min and centrifuged at 3000 × g for 5 min, and transferred the supernatant (membrane extract). We further added the nuclear extraction buffer. After incubating at 4℃ for 30 min and centrifuging at 5000 × g for 5 min, we transferred the supernatant (soluble nuclear extract) fraction. Similarly, we added nuclear extraction buffer containing CaCl2 (5 mM) and micrococcal nuclease (300 units), incubated at room temperature for 15 min, centrifuged at 20,000 × g for 5 min, and transferred the supernatant (chromatin-bound nuclear extract) fraction. Finally, pellet extraction buffer was added in tube. After incubating at room temperature for 10 min and centrifuging at 20,000 × g for 5 min, we obtained the supernatant (i.e., the cytoskeletal extract). All of the buffers were supplemented with protease inhibitor and RNase inhibitor. |
Sample Information
| BioProject | Sample Name | Localization | Treatment | Time | Source | Label |
|---|---|---|---|---|---|---|
| PRJNA850166 | GSM6251220 | SNE (soluble nuclear extract) | mesoderm differentiation | Day 3 | H1 hESC | hESC, SNE (soluble nuclear extract), Day3, rep1 [D10-1_RRL21043-V] |
| PRJNA850166 | GSM6251221 | SNE (soluble nuclear extract) | mesoderm differentiation | Day 3 | H1 hESC | hESC, SNE (soluble nuclear extract), Day3, rep2 [D10-2_RRL21044-V] |
| PRJNA850166 | GSM6251222 | CBNE (chromatin-bound nuclear extract) | mesoderm differentiation | Day 3 | H1 hESC | hESC, CBNE (chromatin-bound nuclear extract), Day3, rep1 [D11-1_RRL21045-V] |
| PRJNA850166 | GSM6251223 | CBNE (chromatin-bound nuclear extract) | mesoderm differentiation | Day 3 | H1 hESC | hESC, CBNE (chromatin-bound nuclear extract), Day3, rep2 [D11-2_RRL21046-V] |
| PRJNA850166 | GSM6251224 | PE (pellet extract) | mesoderm differentiation | Day 3 | H1 hESC | hESC, PE (pellet extract), Day3, rep1 [D12-1_RRL21047-V] |
| PRJNA850166 | GSM6251225 | PE (pellet extract) | mesoderm differentiation | Day 3 | H1 hESC | hESC, PE (pellet extract), Day3, rep2 [D12-2_RRL21048-V] |
| PRJNA850166 | GSM6251226 | INPUT | mesoderm differentiation | Day 3 | H1 hESC | hESC, INPUT, Day3, rep1 [D7-1_RRL21037-V] |
| PRJNA850166 | GSM6251227 | INPUT | mesoderm differentiation | Day 3 | H1 hESC | hESC, INPUT, Day3, rep2 [D7-2_RRL21038-V] |
| PRJNA850166 | GSM6251228 | CE (cytoplasmic extract) | mesoderm differentiation | Day 3 | H1 hESC | hESC, CE (cytoplasmic extract), Day3, rep1 [D8-1_RRL21039-V] |
| PRJNA850166 | GSM6251229 | CE (cytoplasmic extract) | mesoderm differentiation | Day 3 | H1 hESC | hESC, CE (cytoplasmic extract), Day3, rep2 [D8-2_RRL21040-V] |
| PRJNA850166 | GSM6251230 | ME (membrane extract) | mesoderm differentiation | Day 3 | H1 hESC | hESC, ME (membrane extract), Day3, rep1 [D9-1_RRL21041-V] |
| PRJNA850166 | GSM6251231 | ME (membrane extract) | mesoderm differentiation | Day 3 | H1 hESC | hESC, ME (membrane extract), Day3, rep2 [D9-2_RRL21042-V] |
| PRJNA850166 | GSM6251232 | INPUT | mesoderm differentiation | Day 5 | H1 hESC | hESC, INPUT, Day5, rep1 [Q13-1_RRL21049-V] |
| PRJNA850166 | GSM6251233 | INPUT | mesoderm differentiation | Day 5 | H1 hESC | hESC, INPUT, Day5, rep2 [Q13-2_RRL21050-V] |
| PRJNA850166 | GSM6251234 | CE (cytoplasmic extract) | mesoderm differentiation | Day 5 | H1 hESC | hESC, CE (cytoplasmic extract), Day5, rep1 [Q14-1_RRL21051-V] |
| PRJNA850166 | GSM6251235 | CE (cytoplasmic extract) | mesoderm differentiation | Day 5 | H1 hESC | hESC, CE (cytoplasmic extract), Day5, rep2 [Q14-2_RRL21052-V] |
| PRJNA850166 | GSM6251236 | ME (membrane extract) | mesoderm differentiation | Day 5 | H1 hESC | hESC, ME (membrane extract), Day5, rep1 [Q15-1_RRL21053-V] |
| PRJNA850166 | GSM6251237 | ME (membrane extract) | mesoderm differentiation | Day 5 | H1 hESC | hESC, ME (membrane extract), Day5, rep2 [Q15-2_RRL21073-V] |
| PRJNA850166 | GSM6251238 | SNE (soluble nuclear extract) | mesoderm differentiation | Day 5 | H1 hESC | hESC, SNE (soluble nuclear extract), Day5, rep1 [Q16-1_RRL21074-V] |
| PRJNA850166 | GSM6251239 | SNE (soluble nuclear extract) | mesoderm differentiation | Day 5 | H1 hESC | hESC, SNE (soluble nuclear extract), Day5, rep2 [Q16-2_RRL21075-V] |
| PRJNA850166 | GSM6251240 | CBNE (chromatin-bound nuclear extract) | mesoderm differentiation | Day 5 | H1 hESC | hESC, CBNE (chromatin-bound nuclear extract), Day5, rep1 [Q17-1_RRL21076-V] |
| PRJNA850166 | GSM6251241 | CBNE (chromatin-bound nuclear extract) | mesoderm differentiation | Day 5 | H1 hESC | hESC, CBNE (chromatin-bound nuclear extract), Day5, rep2 [Q17-2_RRL21077-V] |
| PRJNA850166 | GSM6251242 | PE (pellet extract) | mesoderm differentiation | Day 5 | H1 hESC | hESC, PE (pellet extract), Day5, rep1 [Q18-1_RRL21078-V] |
| PRJNA850166 | GSM6251243 | PE (pellet extract) | mesoderm differentiation | Day 5 | H1 hESC | hESC, PE (pellet extract), Day5, rep2 [Q18-2_RRL21079-V] |
| PRJNA850166 | GSM6251244 | INPUT | None | Day 0 | H1 hESC | hESC, INPUT, Day0, rep1 [W1-1_RRL21025-V] |
| PRJNA850166 | GSM6251245 | INPUT | None | Day 0 | H1 hESC | hESC, INPUT, Day0, rep2 [W1-2_RRL21026-V] |
| PRJNA850166 | GSM6251246 | CE (cytoplasmic extract) | None | Day 0 | H1 hESC | hESC, CE (cytoplasmic extract), Day0, rep1 [W2-1_RRL21027-V] |
| PRJNA850166 | GSM6251247 | CE (cytoplasmic extract) | None | Day 0 | H1 hESC | hESC, CE (cytoplasmic extract), Day0, rep2 [W2-2_RRL21028-V] |
| PRJNA850166 | GSM6251248 | ME (membrane extract) | None | Day 0 | H1 hESC | hESC, ME (membrane extract), Day0, rep1 [W3-1_RRL21029-V] |
| PRJNA850166 | GSM6251249 | ME (membrane extract) | None | Day 0 | H1 hESC | hESC, ME (membrane extract), Day0, rep2 [W3-2_RRL21030-V] |
| PRJNA850166 | GSM6251250 | SNE (soluble nuclear extract) | None | Day 0 | H1 hESC | hESC, SNE (soluble nuclear extract), Day0, rep1 [W4-1_RRL21031-V] |
| PRJNA850166 | GSM6251251 | SNE (soluble nuclear extract) | None | Day 0 | H1 hESC | hESC, SNE (soluble nuclear extract), Day0, rep2 [W4-2_RRL21032-V] |
| PRJNA850166 | GSM6251252 | CBNE (chromatin-bound nuclear extract) | None | Day 0 | H1 hESC | hESC, CBNE (chromatin-bound nuclear extract), Day0, rep1 [W5-1_RRL21033-V] |
| PRJNA850166 | GSM6251253 | CBNE (chromatin-bound nuclear extract) | None | Day 0 | H1 hESC | hESC, CBNE (chromatin-bound nuclear extract), Day0, rep2 [W5-2_RRL21034-V] |
| PRJNA850166 | GSM6251254 | PE (pellet extract) | None | Day 0 | H1 hESC | hESC, PE (pellet extract), Day0, rep1 [W6-1_RRL21035-V] |
| PRJNA850166 | GSM6251255 | PE (pellet extract) | None | Day 0 | H1 hESC | hESC, PE (pellet extract), Day0, rep2 [W6-2_RRL21036-V] |
| PRJNA850166 | GSM6251256 | cytoplasm | None | Day 0 | H1 hESC | hESC, cytoplasm, Day0, rep1 [D0_cytoplasm-1] |
| PRJNA850166 | GSM6251257 | cytoplasm | None | Day 0 | H1 hESC | hESC, cytoplasm, Day0, rep2 [D0_cytoplasm-2] |
| PRJNA850166 | GSM6251258 | nucleus | None | Day 0 | H1 hESC | hESC, nucleus, Day0, rep1 [D0_nucleus-1] |
| PRJNA850166 | GSM6251259 | nucleus | None | Day 0 | H1 hESC | hESC, nucleus, Day0, rep2 [D0_nucleus-2] |
Subcellular Localization Number
RNA Type:
Condition:
Localization Differential Analysis
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Enrichment:
Specific Subcellular Localization
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Dynamic RNA Localization
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Specific Enrichment Analysis
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Enrichment:
Specific RNA Ratio
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RNA Symbol:
TPM:
