|
| Status |
Public on Nov 28, 2012 |
| Title |
Wild-type, Replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
yeast mRNA extract
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain background: BY4741
genotype/variation: Wild-type
|
| Treatment protocol |
No treatment (conditions lack G418)
|
| Growth protocol |
YPD; log-growth from OD 0.2 to 1.0 at 30*C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Hybrid Trizol Reagent RNA extraction and RNEAsy column purification
mRNA were purified via Oligo-DT dynabeads twice; purified mRNA were fragmented to yield fragments averaging 200-300-bp.Illumina adapters were then ligated and amplified, followed by size-selection and qPCR quantitation.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Base-calling provided by Illumina stock software. Details on what is used by the UCSD core can be found at microarrays.ucsd.edu
Reads were aligned via Bowtie 0.12.5 with the following arguments (-m 1 -B 1)
Data were filtered to only accept non-clonal reads
Counts for each ORF were tallied as the median number of non-clonal reads overallping positions in the last 200 bases of each yeast ORF (Nagalakshmi, 2011)
Genome_build: scerevisiae genome downloaded from SGD in 06/2012
Supplementary_files_format_and_content: tab-delimited file contains a matrix with each row representing each yeast ORF and each column representing RNA-Seq measurements in each experiment. Each cell reports the number of counts observed in the corresponding experiment for the corresponding ORF.
|
| |
|
| Submission date |
Nov 27, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Menzies Chen |
| E-mail(s) |
mec001@ucsd.edu
|
| Organization name |
UCSD
|
| Department |
Bioengineering
|
| Lab |
Ideker Lab
|
| Street address |
9500 Gilman Drive MC 0688
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL13821 |
| Series (1) |
| GSE42554 |
Decoupling epigenetic and genetic effects through systematic analysis of gene position |
|
| Relations |
| SRA |
SRX206553 |
| BioSample |
SAMN01819925 |
