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| Status |
Public on Jun 01, 2022 |
| Title |
5-CA-cys4-d |
| Sample type |
SRA |
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| Source name |
Candida albicans
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| Organism |
Candida albicans |
| Characteristics |
strains: Candida albicans cys4 mutant
genotype: cys4::hisG/ cys4::hisG-URA3-hisG ura3::imm434/ura3::imm434
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| Treatment protocol |
Overnight grown C. albicans CAF2-1, cys4Δ/Δ, cys4Δ/Δ+CYS4 cells were diluted to 1E6 cells per milliliter using RPMI1640 medium and cultured for 5 h at 37 ℃.
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| Growth protocol |
Overnight grown C. albicans CAF2-1, cys4Δ/Δ, cys4Δ/Δ+CYS4 cells were diluted to 1E6 cells per milliliter using RPMI1640 medium and cultured for 5 h at 37 ℃.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using a RiboPure-Yeast kit (Ambion) following the manufacturer’s instructions.
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 |
HiSeq X Ten |
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| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
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| Submission date |
Sep 16, 2019 |
| Last update date |
Jun 01, 2022 |
| Contact name |
Wenqiang Chang |
| E-mail(s) |
changwenqiang@sdu.edu.cn
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| Phone |
+8653188382162
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| Organization name |
Shandong University
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| Street address |
No. 44 West Wenhua Road
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| City |
Jinan |
| State/province |
Shandong |
| ZIP/Postal code |
250012 |
| Country |
China |
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| Platform ID |
GPL27466 |
| Series (1) |
| GSE137530 |
Next generation sequencing facilitates quantitative analysis of transcriptional profiling of Candida albicans wild type and cys4 mutant strains |
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| Relations |
| BioSample |
SAMN12768344 |
| SRA |
SRX6854867 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4081377_cys4_d2.txt.gz |
60.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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