|
| Status |
Public on Oct 21, 2016 |
| Title |
cyr1∆/∆::CYR1 pH 7 replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
cyr1∆/∆::CYR1 pH 7
|
| Organism |
Candida albicans |
| Characteristics |
parental strain: SC5314
genotype: cyr1 delta/delta:: CYR1
medium ph: 7
|
| Treatment protocol |
Growth in 10 ml YNB medium/0.2% glucose/5mM GlcNAc/50mM citrate at pH 4 or pH 7 for 4 hours with shaking at 37C. 5ml used for RNA isolation
|
| Growth protocol |
Cells were grown overnight in YPD and back-diluted into treatment medium at 1.5*10^7 cells per ml in 10 mls per tube
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were pelleted by centrifugation at 5k RPM for 5 minutes and RNA was extracted from cells using the Epicentre Yeast RNA extraction kit and subjected to RNA seq
mRNA was enriched by hybridization to oligo dT beads. Directional RNAseq libraries were prepared with TruSeq Stranded mRNA Library Prep chemistry with unique TruSeq indexes, using an automated liquid-handling system. Libraries were pooled and sequenced on a NextSeq500 instrument, 2X75bp PE sequencing (high-output flow cell).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Mutant derivatives of wild-type strain SC5314
|
| Data processing |
Reads were trimmed for adaptor sequences and mapped to the Candia albicans SC5314 whole genome with CLC Genomics Workbench platform (v8.5.1) using default parameters.
Mapped reads were quantile normalized to all reads using CLC Genomics Workbench.
Genome_build: C_albicans_SC5314_version_A21-s02-m09-r04
Supplementary_files_format_and_content: Processed data file is a data matrix that contains raw unique gene reads and quantile normalized reads.
|
| |
|
| Submission date |
Sep 07, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Deborah A Hogan |
| E-mail(s) |
dhogan@dartmouth.edu
|
| Organization name |
Dartmouth College
|
| Department |
Microbiology and Immunology
|
| Lab |
Hogan
|
| Street address |
HB7550
|
| City |
Hanover |
| State/province |
NH |
| ZIP/Postal code |
03755 |
| Country |
Germany |
| |
|
| Platform ID |
GPL22403 |
| Series (1) |
| GSE86540 |
Effects of pH on the transcriptional profile of adenylate cyclase (cyr1) mutants |
|
| Relations |
| BioSample |
SAMN05736615 |
| SRA |
SRX2146086 |
