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Sample GSM447580 Query DataSets for GSM447580
Status Public on Sep 10, 2009
Title mRNA-dcr1KO-1
Sample type SRA
 
Source name log-phase liquid culture, ∆dcr1
Organism Naumovozyma castellii
Characteristics strain: DPB009
rnai deletion: ∆dcr1
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 SRX012930
BioSample SAMN00005073

Supplementary file Size Download File type/resource
GSM447580.txt.gz 35.4 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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