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| Status |
Public on Jul 27, 2015 |
| Title |
LIN28A modulates splicing and gene expression programs in breast cancer cells [RIP-Seq] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
The goals of this study were to identify LIN28 downstream gene targets in breast cancer cells. We use a subclone of the MCF-7 breast cancer cell line, MCF-7M as our model system.
Methods: mRNA-protein complexes (mRNP) lysates were prepared from MCF-7M cells and incubated with Protein-A Sepharose beads (Sigma-Aldrich) and either LIN28 (Abcam) or control normal rabbit serum IgG antibodies. LIN28 interacting mRNAs were identified by whole genome sequencing.
Results: Using an optimized data analysis workflow, we mapped approximately 13 million sequence reads for LIN28-IP and CTL- IP (IgG), respectively to the to the human genome (build h19).
Conclusions: mRNA were significantly bound by LIN28 if LIN28 RIP had 2.5 fold increase in normalized reads compared to IgG. We found that LIN28 was predominantly bound at coding exons and 3'UTRs, 38% & 45% respectively, in the 843 mRNAs within MCF-7M genome.
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| Overall design |
LIN28 mRNA enriched regions identified from LIN28/RNA complexes prepared from MCF-7M cells.
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| Contributor(s) |
Archer TK |
| Citation(s) |
26149387 |
| Submission date |
Jul 16, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Trevor Archer |
| E-mail(s) |
archer1@niehs.nih.gov
|
| Organization name |
NIH
|
| Lab |
ESCBL
|
| Street address |
111 TW Alexander
|
| City |
RTP |
| ZIP/Postal code |
27709 |
| Country |
USA |
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| Platforms (1) |
| GPL9052 |
Illumina Genome Analyzer (Homo sapiens) |
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| Samples (2) |
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| This SubSeries is part of SuperSeries: |
| GSE71013 |
LIN28A modulates splicing and gene expression programs in breast cancer cells |
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| Relations |
| BioProject |
PRJNA290096 |
| SRA |
SRP061241 |
