|
| Status |
Public on Jun 01, 2020 |
| Title |
GUT_YPD_3 |
| Sample type |
SRA |
| |
|
| Source name |
in vitro culture
|
| Organism |
Candida albicans |
| Characteristics |
strain: SN928
time post inoculation: 4 hours
growth condition: YEPD, 30C
|
| Growth protocol |
Candida albicans strains were grown in YEPD media overnight, then diluted to OD=0.1 and grown for 4 hours to an OD=1. These log phase cultures were either pelleted and snap frozen or used for oral gavage of mice. For mouse colonization, mice were given autoclaved food and water with penicillin and streptomycin ad libitum throughout the colonization. C. albicans colonization in mice was maintained for 10 days until the euthanization of the animals.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Acid phenol extraction followed by phenol-chloroform extraction, isopropanol preciptation, followed by SPRI bead cleanup
Followed standard protocol for NEBNext Ultra Directional Library Preparation
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Reads In fastq files were aligned to C. albicans transcriptome using kallisto with default parameters
Estimated counts generated from kallisto for each fastq were extracted and pair-wise comparisons between biological conditions was performed with limma using growth condition and batch as parameters in the design matrix
Supplementary_files_format_and_content: White_opaque_regulator_RNA_expression.xlsx contains log2 fold changes and adjusted p-values of pair-wise comparisons performed in limma; White_opaque_regulator_estimated_counts.xlsx contains estimated counts generated by kallisto that were used as input to limma
|
| |
|
| Submission date |
May 19, 2020 |
| Last update date |
Jun 01, 2020 |
| Contact name |
Suzanne M Noble |
| E-mail(s) |
suzanne.noble@ucsf.edu
|
| Organization name |
UCSF
|
| Street address |
513 Parnassus Ave., Box 0414
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143-0414 |
| Country |
USA |
| |
|
| Platform ID |
GPL24129 |
| Series (2) |
| GSE150855 |
Candida albicans sexual regulators control expression of genes important for commensal fitness [RNA-seq] |
| GSE150879 |
Recording of DNA binding events during gut commensalism reveals the action of a repurposed Candida albicans regulatory network |
|
| Relations |
| BioSample |
SAMN14972431 |
| SRA |
SRX8363500 |
