|
| Status |
Public on Sep 10, 2009 |
| Title |
mRNA-ago1KO-1 |
| Sample type |
SRA |
| |
|
| Source name |
log-phase liquid culture, ∆ago1
|
| Organism |
Naumovozyma castellii |
| Characteristics |
strain: DPB007
rnai deletion: ∆ago1
|
| Growth protocol |
Two biological replicates of yeast strains DPB005 (WT), DPB007 (∆ago1), and DPB009 (∆dcr1) were grown at 25°C in YPD to OD600 0.6–0.8.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA isolated using hot phenol was treated with DNaseI. Poly-(A)+ mRNA was purified from total RNA using magnetic oligo-dT beads, and then fragmented by alkaline hydrolysis. RNA fragments (25–45 nt) were gel-purified and 3´-dephosphorylated with T4 PNK in MES-NaOH buffer. After phenol extraction and precipitation, RNA was ligated to pre-adenylated adaptor DNA. Gel-purified ligation products were 5´-phosphorylated with T4 PNK. After phenol extraction and precipitation, RNA was ligated to a 5´-adaptor RNA, gel-purified, converted to cDNA, amplified, and sequenced.
|
| |
|
| 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 |
Sep 01, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
David Eric Weinberg |
| E-mail(s) |
david.weinberg@ucsf.edu
|
| Phone |
415-514-9723
|
| Organization name |
University of California, San Francisco
|
| Lab |
Weinberg
|
| Street address |
600 16th Street, GH S572F
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
| |
|
| Platform ID |
GPL15027 |
| Series (2) |
| GSE17870 |
The impact of RNAi on the Saccharomyces castellii transcriptome |
| GSE17872 |
RNAi in budding yeast |
|
| Relations |
| SRA |
SRX012928 |
| BioSample |
SAMN00005071 |
