|
Status |
Public on Aug 10, 2011 |
Title |
RNAseq_S.cerevisiae_AGO1 |
Sample type |
SRA |
|
|
Source name |
log-phase liquid culture, AGO1
|
Organism |
Saccharomyces cerevisiae |
Characteristics |
strain: DPB252 genotype/variation: AGO1
|
Growth protocol |
Liquid cultures were grown at 30ÂșC 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 |
SRX092296 |
BioSample |
SAMN00710307 |