|
| Status |
Public on Aug 12, 2016 |
| Title |
WT |
| Sample type |
SRA |
| |
|
| Source name |
yeast cultures
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain genotype: MATa; ura3-1; trp1delta 2; leu2-3,112; his3-11,15; ade2-1; can1-100
genetic background: BMA64
mating type: alpha
|
| Treatment protocol |
Cultures were harvested in log phase with no treatment.
|
| Growth protocol |
cultures were grown in YPD (1% yeast extract, 2% bacto-peptone, 2% dextrose) at 30°C at 200 rpm and harvested at OD 0.4 to 0.6
|
| Extracted molecule |
total RNA |
| Extraction protocol |
All cultures were harvested by centrifugation at 4000 rpm for 2 minutes, washed in deionized water, and spun down in microcentrifuge tubes. The supernatant was removed and pellets were flash-frozen in liquid nitrogen and stored at -80°C. RNA was extracted by standard phenol/chloroform extraction and DNase I-treated.
RNA was sequenced by directly loading onto oligo-dT flow cells, thus no library preparation is involved.
3´-end sequencing of poly(A)+ RNA
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Helicos HeliScope |
| |
|
| Data processing |
Reads were mapped by SeqLL, LLC to the R64-2-1 version of the S.cerevisiae genome obtained from the Saccharomyces genome database (SGD) with the HeliSphere mapping pipeline using default parameters (minlen=15 minscore=4.3 bo=1 ga=none) and only uniquely mapped reads were allowed.
SeqLL, LLC provided bam files of mapped reads, which were converted to sam files with samtools view function.
5´ ends of reads at each chromosomal coordinate were aggregated to generate bedgraphs with the bedtools v2.25.0 genomecov function.
Mapped positions were first filtered for A/G richness in the immediate genomic region downstream. Poly(A) sites with six genomically encoded A nucleotides downstream (with up to two G nucleotides) were flagged as potential internal oligo-dT mis-priming events and excluded from the analysis.
3´-end sequencing can only determine poly(A) sites to a precision based on the length of homo-adenosines encoded within the genome, so remaining poly(A) sites with the first sequenced nucleotide being an A were shifted to the nearest upstream non-adenosine.
The total reads for each bedgraph (both strands combined) remaining after filtering steps were normalized to 1 million.
Genome_build: R64-2-1 version of the S288C genome of S.cerevisiae (Saccharomyces genome database)
Supplementary_files_format_and_content: bedgraph with each strand separate
|
| |
|
| Submission date |
Dec 01, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Kevin Roy |
| E-mail(s) |
[email protected]
|
| Organization name |
UCLA
|
| Department |
Chemistry and Biochemistry
|
| Lab |
Guillaume Chanfreau
|
| Street address |
607 Charles E. Young Drive East
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL17245 |
| Series (2) |
| GSE75584 |
3´-end sequencing of poly(A)+ RNA in wild-type Saccharomyces cerevisiae and a strain carrying a deletion of the RRP6 nuclear exosome catalytic component |
| GSE75587 |
Nuclear exosome |
|
| Relations |
| BioSample |
SAMN04305357 |
| SRA |
SRX1457887 |
