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| Status |
Public on Sep 10, 2009 |
| Title |
mRNA-WT-1 |
| Sample type |
SRA |
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| Source name |
log-phase liquid culture, WT
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| Organism |
Naumovozyma castellii |
| Characteristics |
strain: DPB005
rnai deletion: WT
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| 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.
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
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| Description |
Small RNA sequencing by mRNA fragmentation, 5' and 3' adaptor ligation, and RT-PCR
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| 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.
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| Submission date |
Sep 01, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
David Eric Weinberg |
| E-mail(s) |
david.weinberg@ucsf.edu
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| Phone |
415-514-9723
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| Organization name |
University of California, San Francisco
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| Lab |
Weinberg
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| Street address |
600 16th Street, GH S572F
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| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
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| Platform ID |
GPL15027 |
| Series (2) |
| GSE17870 |
The impact of RNAi on the Saccharomyces castellii transcriptome |
| GSE17872 |
RNAi in budding yeast |
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| Relations |
| SRA |
SRX012926 |
| BioSample |
SAMN00005069 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM447576.txt.gz |
38.2 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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