|
| Status |
Public on Aug 20, 2015 |
| Title |
RNA-Seq of rpd3 DS cells-2 |
| Sample type |
SRA |
| |
|
| Source name |
Δrpd3 DS cells
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain background: W303
genotype/variation: delta-rpd3
isolate number: isolate 2
conditions at harvest: diauxic shift cells
equivalents of ercc spike: 1
|
| Treatment protocol |
Cells were subject to grinding with glass beads under liquid nitrogen
|
| Growth protocol |
log cells were grown to OD600 0.4 to 0.6; DS cells were harvested 2 hours after glucose exhaustion; Q cells were purified from 7-day stationary phase cultures with a Percoll gradient
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with hot acid phenol, treated with Dnase I, combined with ERCC Spike-in control and depleted of rRNA
Strand-specific libraries were prepared according to dUTP method and TruSeq (Illumina) Sample Prep Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Data processing |
Basecalling was performed by Illumina CASAVA software package
Reads were mapped to S. cerevisiae genome (Saccharomyces_cerevisiae.EF4.65.dna.toplevel.fa) appended with ERCC Spike-in Control reads (https://tools.lifetechnologies.com/content/sfs/manuals/ERCC92.zip) using TopHat2
Mapped reads were filtered using SAMtools flags -f 3 -F 256
Differential transcript analysis was performed using CuffDiff (cufflinks 2.2.1) with a maskfile for rRNA and tRNA
Data were normalized such that ERCC control transcript abundance was equal across samples
Data were scaled to reflect RNA content per cell with scaling factors of: 1.0 for WT Q, 2.5 for WT DS, 5.0 for WT Log, 3.0 for rpd3 Q, 3.5 for rpd3 DS, 5.0 for rpd3 Log
Independent isolates were merged
Genome_build: Saccharomyces_cerevisiae.EF4.65
Supplementary_files_format_and_content: Normalized FPKM Values Correcting for External Spike-in Control and RNA per Cell
|
| |
|
| Submission date |
Mar 23, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Jeffrey N McKnight |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Oregon
|
| Department |
Institute of Molecular Biology
|
| Lab |
McKnight Lab
|
| Street address |
1229 University of Oregon, 1318 Franklin Blvd, Rm 273 Onyx Bridge
|
| City |
Eugene |
| State/province |
OR |
| ZIP/Postal code |
97408 |
| Country |
USA |
| |
|
| Platform ID |
GPL9134 |
| Series (2) |
| GSE67149 |
Strand-Specific RNA Sequencing for wild type and Drpd3 yeast entering quiescence [RNA-seq] |
| GSE67151 |
Rpd3 drives transcriptional quiescence |
|
| Relations |
| BioSample |
SAMN03437080 |
| SRA |
SRX964188 |
