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| Status |
Public on Oct 04, 2017 |
| Title |
WT CO2-1 |
| Sample type |
SRA |
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| Source name |
candida albicans
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| Organism |
Candida albicans |
| Characteristics |
genotype: wild type
growth condition: 5% CO2
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| Growth protocol |
Cells of the WT and sfl2/sfl2 mutant were first grown at 25°C in liquid Lee’s glucose medium for 24 h, then spread onto YPD medium plates and incubated at 37°C in air or in 5% CO2 for 22 h.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were lysed by Mini-beadbeater and total RNA was harvested using GeneJET RNA Purification Kit (Thermo Scientific #K0731, #K0732)
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Illumina OLB_1.9.4 were used for basecalling
Filter dirty raw reads by removing reads with adaptors and low quality, the obtained clean reads were mapped to reference sequences using SOAPaligner/soap2 according to Li et al., Bioinformatics, 2009. Mismatches no more than 2 bases were allowed in the alignment.
Relative gene expression levels were calculated using the FPKM (Fragments Per kb per Million reads) method; FPKM=106C/(NL/103), where “C” is the number of fragments that uniquely aligned to gene A, “N” represents the total number of fragments that uniquely aligned to all genes, and “L” is the number of bases of gene A.
Genome_build: Candida albicans SC5314 genome (ASM18296v1)
Supplementary_files_format_and_content: Excel file containing FPKM and count values for all samples
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| Submission date |
Jul 30, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
guanghua huang |
| Organization name |
Institute of Microbiology
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| Street address |
NO.1 West Beichen Road, Chaoyang District
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| City |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
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| Platform ID |
GPL15645 |
| Series (1) |
| GSE102039 |
Integration of the tricarboxylic acid (TCA) cycle with cAMP signaling and Sfl2 pathways in the regulation of CO2 sensing, filamentation, and virulence in Candida albicans |
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| Relations |
| BioSample |
SAMN07426771 |
| SRA |
SRX3048896 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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