Basic Information
| Dataset | GSE63189 |
|---|---|
| Status | 2015-07-30 |
| Species | Homo sapiens |
| Source | NCBI GEO |
| Subcellular Localization | cytoplasm|nuclear|chromatin |
| PMID | 26236012 |
| Title | Identification and functional characterization of long noncoding RNAs in breast cancer |
| Citation | Sun M, Gadad SS, Kim DS, Kraus WL. Discovery, Annotation, and Functional Analysis of Long Noncoding RNAs Controlling Cell-Cycle Gene Expression and Proliferation in Breast Cancer Cells. Mol Cell 2015 Aug 20;59(4):698-711. |
| Experimental Design | Prior to all treatments, the cells were grown for 3 days in phenol red-free MEM Eagle medium supplemented with 5% charcoal-dextran-treated calf serum. Cell fractionation - all treatments were performed for 180 min with 100 nM 17β-estradiol. Adherent cells were trypsinized, collected, and subsequently lysed in buffer A. The nuclei were collected by gentle centrifugation at 4°C and the resulting supernatant was collected as the cytoplasmic fraction. The nuclear pellet was washed twice with buffer A, each time accompanied by 10 strokes of douncing, to obtain clean and intact nuclei. The nuclei were then extracted with the sequential addition of low salt buffer and high salt buffer. The soluble extract was collected as the nuclear fraction. The remaining pellet was then resuspended in cell disruption buffer (PARIS kit, Ambion; AM1921), digested with DNase I (Roche), and centrifuged to remove any remaining insoluble material. The resulting supernatant was collected as the chromatin fraction. For lncRNA knockdown RNA-seq, transient RNAi-mediated knockdown of lncRNAs was performed by transfection of (1) siRNAs targeting selected lncRNAs and (2) commercially available control siRNA. |
Sample Information
| BioProject | Sample Name | Localization | Treatment | Source | Label |
|---|---|---|---|---|---|
| PRJNA266932 | GSM1543653 | cytoplasmic fraction | Untreated | MCF-7 cells | polyA+ RNA from the cytoplasmic fraction-E2, rep 1 |
| PRJNA266932 | GSM1543654 | cytoplasmic fraction | Untreated | MCF-7 cells | polyA+ RNA from the cytoplasmic fraction-E2, rep 2 |
| PRJNA266932 | GSM1543655 | cytoplasmic fraction | E2 treated | MCF-7 cells | polyA+ RNA from the cytoplasmic fraction+E2, rep 1 |
| PRJNA266932 | GSM1543656 | cytoplasmic fraction | E2 treated | MCF-7 cells | polyA+ RNA from the cytoplasmic fraction+E2, rep 2 |
| PRJNA266932 | GSM1543657 | nuclear fraction | Untreated | MCF-7 cells | polyA+ RNA from the nuclear fraction-E2, rep 1 |
| PRJNA266932 | GSM1543658 | nuclear fraction | Untreated | MCF-7 cells | polyA+ RNA from the nuclear fraction-E2, rep 2 |
| PRJNA266932 | GSM1543659 | nuclear fraction | E2 treated | MCF-7 cells | polyA+ RNA from the nuclear fraction+E2, rep 1 |
| PRJNA266932 | GSM1543660 | nuclear fraction | E2 treated | MCF-7 cells | polyA+ RNA from the nuclear fraction+E2, rep 2 |
| PRJNA266932 | GSM1543661 | chromatin fraction | Untreated | MCF-7 cells | polyA+ RNA from the chromatin fraction-E2, rep 1 |
| PRJNA266932 | GSM1543662 | chromatin fraction | Untreated | MCF-7 cells | polyA+ RNA from the chromatin fraction-E2, rep 2 |
| PRJNA266932 | GSM1543663 | chromatin fraction | E2 treated | MCF-7 cells | polyA+ RNA from the chromatin fraction+E2, rep 1 |
| PRJNA266932 | GSM1543664 | chromatin fraction | E2 treated | MCF-7 cells | polyA+ RNA from the chromatin fraction+E2, 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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