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| Status |
Public on Jul 16, 2014 |
| Title |
LM2_7hr_2_2_RNA-seq |
| Sample type |
SRA |
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| Source name |
MDA-LM2
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| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-LM2
time-point: 7
rep: 4
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| Treatment protocol |
Cells were treated with 4sU for 2-hours. After the pulse-period, the media was replaced with fresh media plus excess Uridine.
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| Growth protocol |
Cells were grown in DMEM-based media supplemented with 10% FBS, 1% L-glutamine, 1% Sodium Pyruvate, and 1% Pen/Strep
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted, labeled and precipitated at 0, 2, 4 and 7 hr as described before (Dolken L, et al. 2008, RNA 14(9):1959-1972)
Samples were prepared for RNA-seq using ScriptSeq V2 (Epicentre) per manufacturers instructions.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
4sU labeled/precepitated RNA
processed data file: LM2_decay_rates.txt
processed data file: MDA-LM2_differential_stability.txt
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| Data processing |
Sequence mapping was performed using TopHat with default parameters (build hg18).
Cufflinks, cuffmerge and cuffcompare were used to calculate FPKMs for annotated transcripts.
For each transcript, FPKM values at every time-point were used to calculate a decay rate based on an exponential decay model.
For each transcript, four independent decay rates were measured in MDA-MB-231 cells and four in MDA-LM2 cells. A t-test based score was used to measure differential decay rates for each transcript across the two cell-lines.
Genome_build: hg18
Supplementary_files_format_and_content: Tab delimited files (linked as supplementary files on the Series record) listing the estimated decay rates along with final differential decay rate scores.
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| Submission date |
Aug 07, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Hani Goodarzi |
| Organization name |
UCSF
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| Department |
Biochemistry and Biophysics
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| Street address |
600 16th St, GH S312D
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| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (2) |
| GSE49608 |
Differential transcript stability measurements in MDA-MB-231 vs. MDA-LM2 cells |
| GSE49649 |
Metastasis-suppressor transcript destabilization through TARBP2 binding of mRNA hairpins |
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| Relations |
| BioSample |
SAMN02303685 |
| SRA |
SRX332309 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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