Basic Information
| Dataset | GSE219089 |
|---|---|
| Status | 2023-02-24 |
| Species | Mus musculus |
| Source | NCBI GEO |
| Subcellular Localization | cell body|protrusion |
| PMID | 36859340 |
| Title | RNA localization to protrusions of mouse melanoma YUMM1.7 cells |
| Citation | Norris ML, Mendell JT. Localization of Kif1c mRNA to cell protrusions dictates binding partner specificity of the encoded protein. Genes Dev 2023 Mar 1;37(5-6):191-203. |
| Experimental Design | Comparative gene expression analysis of RNA-seq data from cell protrusions and cell bodies of YUMM1.7 cells. PET Millicell Hanging Cell Culture Inserts with 1 mm pores sized for 6 well plates were coated on the bottom side with 30 ug/mL fibronectin. Fibronectin was diluted in sterile PBS and inserts were coated for 15 minutes, then aspirated and allowed to dry. 6x105 to 8x105 cells were plated per membrane and placed in an incubator overnight. For fractionation, media was aspirated, cells were rinsed with RNase-free PBS and aspirated, then cell bodies were scraped using a cell scraper and collected into Qiazol. Inserts were rinsed with RNase-free PBS and cleaned with a cotton swab three times. The cleaned insert was carefully dislodged, placed inside a new tube with Qiazol and briefly vortexed. After cell bodies and protrusions were collected, the standard protocol the Qiagen miRNeasy kit was followed. RNA was eluted with 30 μl RNase-free water. There were two RNA seq replicates, each with 6 inserts. 0.69 - 9.4 ug Total RNA was extracted for each sample. |
Sample Information
| BioProject | Sample Name | Localization | Source | Label |
|---|---|---|---|---|
| PRJNA907013 | GSM6767513 | cell body | melanoma cells YUMM1.7 | YUMM1.7 cells, cell bodies, biol rep 1 |
| PRJNA907013 | GSM6767514 | cell body | melanoma cells YUMM1.7 | YUMM1.7 cells, cell bodies, biol rep 2 |
| PRJNA907013 | GSM6767515 | protrusion | melanoma cells YUMM1.7 | YUMM1.7 cells, protrusions, biol rep 1 |
| PRJNA907013 | GSM6767516 | protrusion | melanoma cells YUMM1.7 | YUMM1.7 cells, protrusions, biol rep 2 |
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Localization Differential Analysis
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Dynamic RNA Localization
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Specific Enrichment Analysis
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