|
| Status |
Public on Jul 01, 2015 |
| Title |
TR2-14 - rep1 - 0% glucose |
| Sample type |
SRA |
| |
|
| Source name |
cells grown in glucose-starved medium
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
growth protocol: glucose-starved medium
strain: Sigma1278b
growth stage: exponential
harvest time: 2 hours after medium switch
tandem repeat number: 14 repeats
|
| Growth protocol |
Cells were grown in YP medium supplemented with 4% glucose until exponential phase. Half the volume of each culture was harvested and the second half transferred to medium without glucose for 2 hours before harvest.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were lysed with glass beads and total RNA was extracted using the Phenol-Chloroform standard method.
polyA RNA libraries were prepared from 1 ug total RNA using standard illumina protocols and sequenced on an Illumina HiSeq2000
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
glu0-TR2-14.1
TR2_14repeats_0%Glu_FC.txt
|
| Data processing |
Raw reads were filtered using FASTX-Toolkit with Q30 cutoff.
Sequenced reads were trimmed to remove adaptor sequences and low quality reads and then aligned to the S. cerevisiae reference genome (GeneBank version 64) using Tophat 2.0.7 to obtain read numbers
The Trimmed Mean of M-values method (Robinson and Oshlack, Genome Biology 2010) was used to normalize the data and the edgeR Bioconductor package used to determine differentially expressed genes (in each TR2 variant relative to the WT - TR2-63)
Genome_build: SacCer_May2010
Supplementary_files_format_and_content: Tab delimited text files including Log2 fold change in gene expression relative to the WT sample (TR2-63)
|
| |
|
| Submission date |
Jun 23, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Kevin Verstrepen |
| E-mail(s) |
[email protected]
|
| Phone |
0032 16751393
|
| Organization name |
VIB/KULeuven
|
| Street address |
Gaston Geenslaan 1
|
| City |
Leuven |
| ZIP/Postal code |
3001 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL13821 |
| Series (1) |
| GSE70209 |
Variable glutamine-rich repeats modulate the function of the transcriptional regulator SSN6 |
|
| Relations |
| BioSample |
SAMN03787834 |
| SRA |
SRX1070773 |
