Basic Information
| Dataset | GSE192739 |
|---|---|
| Status | 2022-01-03 |
| Species | Homo sapiens |
| Source | NCBI GEO |
| Subcellular Localization | MITO (mitochondrial matrix)|ERM (endoplasmic reticulum membrane)|NES (cytosol)|LMNB1 (nuclear lamina) |
| PMID | 35245437 |
| Title | Metabolic incorporation of electron-rich ribonucleosides enhances APEX-seq for profiling spatially restricted nascent transcriptome |
| Citation | Li R, Zou Z, Wang W, Zou P. Metabolic incorporation of electron-rich ribonucleosides enhances APEX-seq for profiling spatially restricted nascent transcriptome. Cell Chem Biol 2022 Jul 21;29(7):1218-1231.e8. |
| Experimental Design | MERR APEX-seq libraries were generated for the following constructs with APEX2: (1) MITO (mitochondrial matrix), (2) ERM (endoplasmic reticulum membrane), (3) NES (cytosol) and (4) LMNB1 (nuclear lamina). 16 libraries were prepared for MITO before (INPUT) and after (ENRICH) enrichment (2 biological replicates for labeled targets of s6G-APEX-labeling, s4U-APEX-labeling and APEX labeling each and 2 biological replicates for unlabeled control of no metabolism and no probe), 8 libraries were prepared for ERM before (INPUT) and after (ENRICH) enrichment (4 biological replicates for labeled targets of s6G-APEX-labeling), 4 libraries were prepared for NES before (INPUT) and after (ENRICH) enrichment (2 biological replicates for labeled targets of s6G-APEX-labeling) and 12 libraries were prepared for LMNB1 before (INPUT) and after (ENRICH) enrichment (2 biological replicates for labeled targets of s6G-APEX-labeling and APEX labeling each and 2 biological replicates for unlabeled control). |
Sample Information
| BioProject | Sample Name | Localization | Treatment | Source | Label |
|---|---|---|---|---|---|
| PRJNA793004 | GSM5764319 | MITO (mitochondrial matrix) | treated with 100 µM s6G for 5 hr | HEK293T | MITO_s6G_IN_rep1 |
| PRJNA793004 | GSM5764321 | MITO (mitochondrial matrix) | treated with 100 µM s6G for 5 hr | HEK293T | MITO_s6G_IN_rep2 |
| PRJNA793004 | GSM5764322 | MITO (mitochondrial matrix) | treated with 100 µM s6G for 5 hr | HEK293T | MITO_s6G_EN_rep1 |
| PRJNA793004 | GSM5764324 | MITO (mitochondrial matrix) | treated with 100 µM s6G for 5 hr | HEK293T | MITO_s6G_EN_rep2 |
| PRJNA793004 | GSM5764325 | MITO (mitochondrial matrix) | treated with 100 µM s4U for 5 hr | HEK293T | MITO_s4U_IN_rep1 |
| PRJNA793004 | GSM5764326 | MITO (mitochondrial matrix) | treated with 100 µM s4U for 5 hr | HEK293T | MITO_s4U_IN_rep2 |
| PRJNA793004 | GSM5764328 | MITO (mitochondrial matrix) | treated with 100 µM s4U for 5 hr | HEK293T | MITO_s4U_EN_rep1 |
| PRJNA793004 | GSM5764329 | MITO (mitochondrial matrix) | treated with 100 µM s4U for 5 hr | HEK293T | MITO_s4U_EN_rep2 |
| PRJNA793004 | GSM5764331 | MITO (mitochondrial matrix) | untreated | HEK293T | MITO_RNA_IN_rep1 |
| PRJNA793004 | GSM5764332 | MITO (mitochondrial matrix) | untreated | HEK293T | MITO_RNA_IN_rep2 |
| PRJNA793004 | GSM5764334 | MITO (mitochondrial matrix) | untreated | HEK293T | MITO_RNA_EN_rep1 |
| PRJNA793004 | GSM5764335 | MITO (mitochondrial matrix) | untreated | HEK293T | MITO_RNA_EN_rep2 |
| PRJNA793004 | GSM5764337 | MITO (mitochondrial matrix) | untreated | HEK293T | MITO_ctrl_IN_rep1 |
| PRJNA793004 | GSM5764339 | MITO (mitochondrial matrix) | untreated | HEK293T | MITO_ctrl_IN_rep2 |
| PRJNA793004 | GSM5764340 | MITO (mitochondrial matrix) | untreated | HEK293T | MITO_ctrl_EN_rep1 |
| PRJNA793004 | GSM5764342 | MITO (mitochondrial matrix) | untreated | HEK293T | MITO_ctrl_EN_rep2 |
| PRJNA793004 | GSM5764343 | ERM (endoplasmic reticulum membrane) | treated with 100 µM s6G for 5 hr | HEK293T | ERM_s6G_IN_rep1 |
| PRJNA793004 | GSM5764345 | ERM (endoplasmic reticulum membrane) | treated with 100 µM s6G for 5 hr | HEK293T | ERM_s6G_IN_rep2 |
| PRJNA793004 | GSM5764347 | ERM (endoplasmic reticulum membrane) | treated with 100 µM s6G for 5 hr | HEK293T | ERM_s6G_IN_rep3 |
| PRJNA793004 | GSM5764348 | ERM (endoplasmic reticulum membrane) | treated with 100 µM s6G for 5 hr | HEK293T | ERM_s6G_IN_rep4 |
| PRJNA793004 | GSM5764350 | ERM (endoplasmic reticulum membrane) | treated with 100 µM s4U for 5 hr | HEK293T | ERM_s6G_EN_rep1 |
| PRJNA793004 | GSM5764352 | ERM (endoplasmic reticulum membrane) | treated with 100 µM s4U for 5 hr | HEK293T | ERM_s6G_EN_rep2 |
| PRJNA793004 | GSM5764353 | ERM (endoplasmic reticulum membrane) | treated with 100 µM s4U for 5 hr | HEK293T | ERM_s6G_EN_rep3 |
| PRJNA793004 | GSM5764355 | ERM (endoplasmic reticulum membrane) | treated with 100 µM s4U for 5 hr | HEK293T | ERM_s6G_EN_rep4 |
| PRJNA793004 | GSM5764357 | NES (cytosol) | treated with 100 µM s6G for 5 hr | HEK293T | NES_s6G_IN_rep1 |
| PRJNA793004 | GSM5764359 | NES (cytosol) | treated with 100 µM s6G for 5 hr | HEK293T | NES_s6G_IN_rep2 |
| PRJNA793004 | GSM5764360 | NES (cytosol) | treated with 100 µM s6G for 5 hr | HEK293T | NES_s6G_EN_rep1 |
| PRJNA793004 | GSM5764362 | NES (cytosol) | treated with 100 µM s6G for 5 hr | HEK293T | NES_s6G_EN_rep2 |
| PRJNA793004 | GSM5764364 | LMNB1 (nuclear lamina) | treated with 100 µM s4U for 5 hr | HEK293T | LMNB1_s6G_IN_rep1 |
| PRJNA793004 | GSM5764365 | LMNB1 (nuclear lamina) | treated with 100 µM s4U for 5 hr | HEK293T | LMNB1_s6G_IN_rep2 |
| PRJNA793004 | GSM5764367 | LMNB1 (nuclear lamina) | treated with 100 µM s4U for 5 hr | HEK293T | LMNB1_s6G_EN_rep1 |
| PRJNA793004 | GSM5764369 | LMNB1 (nuclear lamina) | treated with 100 µM s4U for 5 hr | HEK293T | LMNB1_s6G_EN_rep2 |
| PRJNA793004 | GSM5764371 | LMNB1 (nuclear lamina) | untreated | HEK293T | LMNB1_RNA_IN_rep1 |
| PRJNA793004 | GSM5764372 | LMNB1 (nuclear lamina) | untreated | HEK293T | LMNB1_RNA_IN_rep2 |
| PRJNA793004 | GSM5764374 | LMNB1 (nuclear lamina) | untreated | HEK293T | LMNB1_RNA_EN_rep1 |
| PRJNA793004 | GSM5764376 | LMNB1 (nuclear lamina) | untreated | HEK293T | LMNB1_RNA_EN_rep2 |
| PRJNA793004 | GSM5764378 | LMNB1 (nuclear lamina) | untreated | HEK293T | LMNB1_ctrl_IN_rep1 |
| PRJNA793004 | GSM5764379 | LMNB1 (nuclear lamina) | untreated | HEK293T | LMNB1_ctrl_IN_rep2 |
| PRJNA793004 | GSM5764381 | LMNB1 (nuclear lamina) | untreated | HEK293T | LMNB1_ctrl_EN_rep1 |
| PRJNA793004 | GSM5764382 | LMNB1 (nuclear lamina) | untreated | HEK293T | LMNB1_ctrl_EN_rep2 |
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Dynamic RNA Localization
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