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Sample GSM5171789 Query DataSets for GSM5171789
Status Public on Dec 27, 2023
Title 0 minute Control, rep2
Sample type SRA
Source name whole organism total RNA
Organism Candida albicans
Characteristics strain: NCCPF 400034
treatment: 0 minutes overnight growth in YPD at 150 RPM (control)
Treatment protocol The overnight grown Candida albicans NCCPF 400034 was then placed in complete human serum (O+ve) supplemented with 1 % butanol and incubated in 5 % CO2 at 37 °C. The cells were then harvested at different time points to extract the total mRNA. The YPD grown Candida cells were treated as control and RNA was sequenced using next generation techniques.
Growth protocol Candida albicans NCCPF 400034 was grown at 37 °C overnight in YPD medium. The cells were then washed with PBS and counted using the hemocytometer.
Extracted molecule total RNA
Extraction protocol RNA was extracted using the Ribopure Yeast Kit (Ambion). The total RNA extraction was performed as per the mannual described in the Kit protocol. Briefly, Candida albicans grown in serum for different time points were washed with the PBS and then the total RNA was extracted using the Ribopure yeast kit. RNA purity was confirmed by the nandrop and RNA integrity were confirmed by analysis on an Agilent 2100 bioanalyzer, using the RNA 6000 nano kit (Agilent) to conform RINs above 8.0. The YPD grown samples was also extracted with the above kit and the RNA purity was checked by Nanodrop.
RNA library was prepared as recommended by the IlluminaTruseq RNA sample preparation kit V2 for serum +butanol grown samples and sequencing was performed using Genome Analyzer IIx for 36 cycles. For the YPD grown sample RNA library was prepared using Ribo-zero gold kit and sequencing was performed on Illumina Hiseq for 150 cycles.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Data processing Illumina Casava1.8 software used for basecalling.
All sequence reads were trimmed off adaptor sequences and YPD grown sample sequence reads wer trimmed to make it 36 base pairs to maintain uniformity across the samples. Sequence reads were independently aligned using QIAGEN CLC Genomics Workbench 21.0.3 with default setting against Candida albicans genome (Assembly 22).
Differential expression, p-value and fold changes for each gene were determined using QIAGEN CLC Genomics Workbench 21.0.3 with default parameters.
Genome_build: Candida albicans SC5314 genome assembly 22.
Supplementary_files_format_and_content: Excel files include RPKM values for each mRNA of respective samples.
Submission date Mar 14, 2021
Last update date Dec 27, 2023
Contact name Agam Prasad Singh
Organization name NII
Department IDL
Street address Aruna Asaf Ali Marg
City New Delhi
State/province Delhi
ZIP/Postal code 110067
Country India
Platform ID GPL28323
Series (1)
GSE168874 Whole genome mRNA expression profiling during Candida albicans growth in complete human serum and butanol
BioSample SAMN18307007
SRA SRX10338794

Supplementary file Size Download File type/resource
GSM5171789_0_minute_Control_2.xlsx 295.8 Kb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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