|
| Status |
Public on Jan 06, 2022 |
| Title |
RNA_WT_S2_pe |
| Sample type |
SRA |
| |
|
| Source name |
WT_S2_pe
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
genotype: WT
condition: glucose starvation
cell source: CEN.PK cells
|
| Treatment protocol |
To perform glucose starvation, we quickly replaced the media by spinning down the cells, washing the pellets with pre-warmed S media, and then resuspending cells in the same volume of warmed S media. Samples were collected at indicated times. Glucose replenishment was carried out at a final concentration of 2% glucose. All centrifugations were performed at 3000 rpm, 2 min at room temperature.
|
| Growth protocol |
Strains of interest were grown in SD medium overnight. Cells from overnight cultures were inoculated into fresh SD to 0.2 optical density (OD)/ml and grown at least two generations to log phase (OD600 ~1).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cells were first quenched in TCA (10% final) and washed with acetone. Cell lysis was performed by bead-beating in urea buffer containing 6 M urea, 1% SDS, 50 mM Tris-HCl pH 7.5, 50 mM NaF, 5 mM EDTA, 1 mM PMSF, and protease inhibitor cocktail (Roche). Supernatants of the lysates were collected after heating for 10 min at 75°C.
RNA isolation of one OD600 unit of cells was performed using MasterPure yeast RNA purification kit (Epicenter) following the manufacturer’s protocol. RNA concentration was determined by A260. 1 mg RNA was reverse transcribed to cDNA using Superscript III Reverse Transcriptase from Invitrogen. Real-time PCR was performed in triplicate with SYBR GreenSuper mix from BioRad.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
wt_gcn5_countTable.logCPM.txt
|
| Data processing |
Reads with phred quality scores less than 20 and less than 35 bp after trimming were removed from further analysis using trimgalore version 0.4.1. Quality-filtered reads were then aligned to the yeast reference genome (S288C) using the HISAT (v 2.0.1) (Pertea et al., 2016) aligner using default settings and marked duplicates using Sambamba version 0.6.6 (Tarasov et al., 2015). Aligned reads were quantified using ‘featurecount’ (v1.4.6) (Liao et al., 2014) per ID against reference annotations (R64-2-1) . Log fold changes were used to calculate KEGG pathway enrichment using clusterProfiler (Chiang et al., 2021).
Genome_build: S288C
Supplementary_files_format_and_content: tab-delimited gene count files
|
| |
|
| Submission date |
Jun 14, 2021 |
| Last update date |
Jan 06, 2022 |
| Contact name |
Wen-Chuan Hsieh |
| E-mail(s) |
[email protected]
|
| Organization name |
UTSouthwestern Medical Center
|
| Department |
Biochemistry
|
| Lab |
Tu lab
|
| Street address |
5323 Harry Hines Blvd
|
| City |
Dallas |
| State/province |
Texas |
| ZIP/Postal code |
75390 |
| Country |
USA |
| |
|
| Platform ID |
GPL27812 |
| Series (2) |
| GSE178160 |
Glucose Starvation Induces a Switch in the Histone Acetylome for Activation of Gluconeogenic and Fat Metabolism Genes [RNA-seq] |
| GSE178161 |
Glucose Starvation Induces a Switch in the Histone Acetylome for Activation of Gluconeogenic and Fat Metabolism Genes |
|
| Relations |
| BioSample |
SAMN19697333 |
| SRA |
SRX11141075 |
