|
| Status |
Public on Jul 01, 2016 |
| Title |
1374 wor1 Glu |
| Sample type |
SRA |
| |
|
| Source name |
wor1 deletion mutant, glucose
|
| Organism |
Candida tropicalis MYA-3404 |
| Characteristics |
strain/background: MYA-3404
genotype/variation: wor1 deletion mutant
medium: Lee's glucose
|
| Growth protocol |
wor1 deletion mutant cells grown in Lee's glucose or Lee's GlcNAc medium.
|
| 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.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| 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.
The gene expression level is calculated by using RPKM method (Reads Per kb per Million reads) according to Mortazavi, et al., Nature Methods, 2008, and the formula is shown as follows: RPKM=106C/(NL/103). C is the number of reads that uniquely aligned to a gene, N is total number of reads that uniquely aligned to all genes, and L is the number of bases on a gene.
Genome_build: C. tropicalis MYA-3404 genome
Supplementary_files_format_and_content: Tab-delimited text file contains RPKM values.
|
| |
|
| Submission date |
Sep 22, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
guanghua huang |
| Organization name |
Institute of Microbiology
|
| Street address |
NO.1 West Beichen Road, Chaoyang District
|
| City |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
| |
|
| Platform ID |
GPL20946 |
| Series (1) |
| GSE73340 |
Regulation of filamentation in the human fungal pathogen Candida tropicalis |
|
| Relations |
| BioSample |
SAMN04102706 |
| SRA |
SRX1274735 |
