|
Status |
Public on Oct 15, 2023 |
Title |
1 hour after -Pi, biol repl 3 |
Sample type |
SRA |
|
|
Source name |
BG99 (PMID: 10049916)
|
Organism |
Nakaseomyces glabratus |
Characteristics |
cell line: BG99 (PMID: 10049916) genotype: his3-delta(1+161) treatment: 1 hour of -Pi starvation
|
Treatment protocol |
The remaining culture was collected by filtration, washed with equal volume of pre-warmed no phosphate SC media and then released into the pre-warmed no phosphate SC. After 1 hour incubation with shaking at 30 C, three biological replicates of the starved samples were collected in the same way as above.
|
Growth protocol |
C. glabrata wild type cells were grown in SC overnight, diluted into fresh SC the next morning to OD600 = 0.1, grown for another 2-3 hours until the culture reached mid-log phase (OD600∼0.6). At this point, two biological replicates of pre-starvation samples were collected using a cold methanol quenching method (Pieterse et al. 2006; Zhou and O’Shea 2011).
|
Extracted molecule |
polyA RNA |
Extraction protocol |
Briefly, 5 mL of culture was added directly into 7.5 mL of pre-chilled methanol (−50°C) and incubated in an ethanol-dry ice bath at that temperature for at least 20 min. When all samples were in the ethanol-dry ice bath for > 20 minutes, cells were collected by centrifugation and quickly washed with ice-cold water to remove the methanol and resuspended in RNAlater solution (Qiagen, 76104) for at least 2 hours. Cells were centrifuged to remove the RNAlater, flash-frozen in liquid nitrogen and stored at -80 C until RNA-extraction. For each sample, ∼5x10^7 cells were collected and total RNA was extracted using a MasterPure Yeast RNA purification kit (Biosearch Technologies, MPY03100) following the manufacturer’s protocol. RNA-seq libraries were prepared with the TruSeq RNA Library Preparation Kit v2 (Illumina) with the mRNA purification option.
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 4000 |
|
|
Data processing |
The RNA-seq raw reads were mapped to the C. glabrata genome downloaded from the Candida Genome Database (CGD, RRID:SCR_002036, version s02-m02-r09), using Bowtie v1.1.1 (RRID:SCR_005476) with the option ‘-m 1 --best –strata’ The resulting SAM files were sorted using Samtools v1.2 and the number of reads per transcript was counted using Bedtools2 with the option ‘bedtools coverage -a BAM_file -b genome_annotation.bed -S -s sorted -g Chrom.length’, using gene features for C. glabrata downloaded from CGD, version s02-m07-r04 The trimmed mean of M-values (‘TMM’) method in the EdgeR package was used to calculate the normalization factors for scaling the raw library sizes. Then, normalized read counts were log2 transformed and used for downstream analyses. Assembly: CGD, s02-m07-r04 Supplementary files format and content: tab-delimited text file includes raw counts for each sample Supplementary files format and content: tab-delimited text file includes normalized and log2 transformed counts for each sample
|
|
|
Submission date |
Sep 29, 2023 |
Last update date |
Oct 15, 2023 |
Contact name |
Bin He |
E-mail(s) |
emptyhb@gmail.com, bin-he@uiowa.edu
|
Organization name |
the University of Iowa
|
Department |
Biology
|
Lab |
Gene Regulatory Evolution
|
Street address |
129 East Jefferson St., Biology Building 450
|
City |
Iowa City |
State/province |
IA |
ZIP/Postal code |
52242 |
Country |
USA |
|
|
Platform ID |
GPL33801 |
Series (1) |
GSE244380 |
Divergence of TORC1-mediated Stress Response Leads to Novel Acquired Stress Resistance in a Pathogenic Yeast |
|
Relations |
BioSample |
SAMN37609337 |
SRA |
SRX21934523 |