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| Status |
Public on Jan 18, 2018 |
| Title |
Ca_WT_pH7.6_2 |
| Sample type |
SRA |
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| Source name |
Ca_WT_pH7.6
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| Organism |
Candida albicans |
| Characteristics |
strain: SC5314
genotype/variation: wild type
ph: 7.6
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| Growth protocol |
Each strain (SC5314, DAY25 and CGY1) was precultured overnight in liquid YPD medium at 30°C with agitation and then diluted to an OD600 of 0.1 in SC medium buffered at pH 7.6 or pH 4 with HEPES or citrate buffer,respectively. Cells were incubated at 30°C with agitation until an OD600 of 0.6 to 0.8 was reached and then were collected by centrifugation
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| Extracted molecule |
total RNA |
| Extraction protocol |
MasterPure Yeast RNA purification kit (Epicentre) according to the manufacturer’s instructions.
standard RNA-Seq methods and Illumina technology
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
WT, pH 7.6, replicate 2
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| Data processing |
Reads were quality-checked using FastQC before and after cleaning by Trimmomatic applying default parameters (Bolger et al., 2014).
Reads were then aligned to the C. albicans SC5314 Assembly22 genome (C_albicans_SC5314_A22-s05-m05-r18_haploid, Candida Genome Database, www.candidagenome.org) using Bowtie2 (Langmead and Salzberg, 2012).
Raw read counts for each gene were calculated using HTSeqCount (Anders et al., 2015).
Read count data were analyzed using standard differential analysis pipeline proposed by the DESeq2 R-package.
Genome_build: C_albicans_SC5314_A22-s05-m05-r18_haploid (Candida Genome Database, www.candidagenome.org)
Supplementary_files_format_and_content: Tab-delimited text files. Include raw read counts for each gene calculated using HTSeqCount
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| Submission date |
Jan 17, 2018 |
| Last update date |
Jan 24, 2018 |
| Contact name |
Cécile Garnaud |
| E-mail(s) |
cgarnaud@chu-grenoble.fr
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| Organization name |
CHU Grenoble Alpes
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| Street address |
CS10217
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| City |
Grenoble Cedex 9 |
| ZIP/Postal code |
38043 |
| Country |
France |
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| Platform ID |
GPL19036 |
| Series (1) |
| GSE109291 |
RNA-SEQ analysis of a C. albicans rim101-/- disrupted strain, a strain overexpressing RIM101 and a reference strain at both alkaline (7.6) and acidic (4) pH |
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| Relations |
| BioSample |
SAMN08369933 |
| SRA |
SRX3586234 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2936626_SC5314_pH7_2_htseq.txt.gz |
27.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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