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Sample GSM7814520 Query DataSets for GSM7814520
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

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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