|
| Status |
Public on Apr 02, 2014 |
| Title |
150 minutes after rapamycin addition, biological replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
150 minutes after rapamycin addition to induce depletion of Rpb1 from the nucleus
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: JGY2000
agent: rapamycin
time: 150 minutes
|
| Treatment protocol |
Rapamycin was added to induce depletion of Rpb1 from the nucleus
|
| Growth protocol |
Cells were cultured to mid-log phase in YPD medium
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated by the hot acidic phenol method and purified with DNase treatment on Qiagen RNeasy columns.
RNA sequenced directly by Helicos (DRS method); purified RNA was not modified
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Helicos HeliScope |
| |
|
| Description |
Sample 8
For this Sample, the rawest possible data file is not available. It is not possible to obtain the rawest form of the data, as Helicos is now out of business. Helicos supplied the sequence output as an aligned txt file (linked below as a supplementary file). It is the most unmanipulated form of the data and contains the raw reads.
|
| Data processing |
alignment to genome (Helicos Helisphere))
counting of sequence tags by coordinate on each strand (both reps combined)
classification of coordinates by gene on appropriate strand
comparison of read count at each coordinate over time to compute half-lives
Genome_build: SacCer2
Supplementary_files_format_and_content: Tab-delimited .txt file with half-life for each mRNA isoform (one file consolidating data from both reps across all timepoints)
|
| |
|
| Submission date |
Nov 12, 2013 |
| Last update date |
Apr 02, 2014 |
| Contact name |
Zarmik Moqtaderi |
| Organization name |
Harvard Medical School
|
| Department |
BCMP
|
| Lab |
Struhl lab
|
| Street address |
240 Longwood Avenue C2-355
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL17245 |
| Series (1) |
| GSE52286 |
Global analysis of mRNA isoform half-lives: identification of stabilizing and destabilizing elements in yeast |
|
| Relations |
| BioSample |
SAMN02401709 |
