|
| Status |
Public on Jul 24, 2013 |
| Title |
ecm5D_0hrs_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
S. cerevisiae ecm5 deletion strain
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
yeast strain: BY4741 ecm5D
hours h2o2: 0
biol. replicate #: 3
|
| Treatment protocol |
One half of each yeast culture was taken for the 0 hour (T0) sample. H2O2 was added to remaining cultures at a final concentration of 0.4 mM. Samples were taken 0.5 hours after H2O2 addition for the 0.5 hour (T0.5) sample.
|
| Growth protocol |
Saturated overnight cultures of strains (Snt2-Myc, Ecm5-Myc, or BY4741) were diluted in YPD and grown to mid-log phase (OD600=0.3).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was obtained through hot acid phenol extraction (Collart, M. A., and S. Oliviero. 200; Current Prot. Mol. Bio.)
Libraries were prepared according to Illumina's instructions accompanying the TruSeq RNA Sample Preparation Kit (cat # RS-122-2001). After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2000 following the manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
RNA-seq reads were aligned to the SacCer2 genome assembly using TopHat v1.4 with 25 bp segment length
Aligned BAM files were converted to Wig files using IGVtools
Genome_build: sacCer2
|
| |
|
| Submission date |
Dec 18, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
David Allis |
| Organization name |
The Rockefeller University
|
| Department |
Laboratory of Chromatin Biology and Epigenetics
|
| Lab |
Allis Laboratory
|
| Street address |
1230 York Ave Box 78
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL13821 |
| Series (2) |
| GSE42983 |
The yeast Snt2 protein helps coordinate the transcriptional response to hydrogen-peroxide mediated oxidative stress (RNA-seq) |
| GSE43002 |
The yeast Snt2 protein helps coordinate the transcriptional response to hydrogen-peroxide mediated oxidative stress |
|
| Relations |
| SRA |
SRX211396 |
| BioSample |
SAMN01831669 |
