|
| Status |
Public on Aug 10, 2011 |
| Title |
RNAseq_S.cerevisiae_DCR1 |
| Sample type |
SRA |
| |
|
| Source name |
log-phase liquid culture, DCR1
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: DPB255
genotype/variation: DCR1
|
| Growth protocol |
Liquid cultures were grown at 30ºC to log-phase.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using hot phenol from log-phase YPD cultures and treated with DNaseI. Poly-(A)+ mRNA was purified from total RNA using magnetic oligo-dT beads (2 rounds of poly-(A)+ selection), and then fragmented by alkaline hydrolysis. RNA-Seq cDNA libraries were prepared as described in Drinnenberg et al. (2009).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
Small RNA sequencing by mRNA fragmentation, 5' and 3' adaptor ligation, and RT-PCR
|
| Data processing |
The first 25 nt of each 36-nt read were isolated and collapsed into a non-redundant set of 25-nt sequences with occurrence counts. Sequences were mapped to the reference genome, allowing no mismatches and recovering all hits. The processed files are collapsed to unique sequences (1 line per sequence); the second (numeric) value in each column is the number of times each unique sequence was sequenced.
|
| |
|
| Submission date |
Aug 09, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Ines Anna Drinnenberg |
| E-mail(s) |
drinnenb@wi.mit.edu
|
| Organization name |
Whitehead Institute for Biomedical Research
|
| Lab |
Bartel
|
| Street address |
9 Cambridge Center
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL9134 |
| Series (2) |
| GSE31288 |
The impact of RNAi on the Saccharomyces cerevisiae transcriptome |
| GSE31300 |
Compatibility with Killer explains the Rise of RNAi-deficient Fungi |
|
| Relations |
| SRA |
SRX092297 |
| BioSample |
SAMN00710308 |
