|
| Status |
Public on Nov 26, 2020 |
| Title |
Manji_S7 |
| Sample type |
SRA |
| |
|
| Source name |
Met28 Activation
|
| Organism |
Candida albicans |
| Characteristics |
cell type: wild type with Met28 activation
|
| Treatment protocol |
growth in SC-GlcNac medium and untreated
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA isolation was performed as previously described (Tebbji et al, PloSGenetics 2014)
Libraries were prepared according to Illumina's mRNASeq stranded library preparation kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
RNA sequencing reads were pre-processed with the sequence-grooming tool cutadapt version 0.4.1(MARTIN 2011) with the following quality trimming and filtering parameters (`--phred33 --length 36 -q 5 --stringency 1 -e 0.1`). Each set of paired-end reads was mapped against the C. albicans SC5314 haplotype A, version A22 downloaded from the Candida Genome Database (CGD) (www.candidagenome.org) using HISAT2 version 2.0.4. SAMtools was then used to sort and convert SAM files. The read alignments and C. albicans SC5314 genome annotation were provided as input into StringTie v1.3.3 (PERTEA et al. 2015) which returned gene abundances for each sample. We imported gene abundances into R and conducted differential analysis of gene count data using the DESeq2 R package (Love et al. 2014).
Genome_build: C. albicans CAI4 haplotype A, version A22
Supplementary_files_format_and_content: Tab-delimited gene abundances files
|
| |
|
| Submission date |
Nov 25, 2020 |
| Last update date |
Nov 26, 2020 |
| Contact name |
Vanessa Dumeaux |
| E-mail(s) |
vanessadumeaux@gmail.com
|
| Organization name |
Western University
|
| Department |
Anatomy and Cell Biology
|
| Street address |
Elgin Dr
|
| City |
London |
| State/province |
Ontario |
| ZIP/Postal code |
N6G 2V4 |
| Country |
Canada |
| |
|
| Platform ID |
GPL23041 |
| Series (1) |
| GSE162171 |
Modulation of the complex regulatory network for methionine biosynthesis in fungi |
|
| Relations |
| BioSample |
SAMN16913803 |
| SRA |
SRX9583867 |
