|
| Status |
Public on Dec 31, 2018 |
| Title |
Screen 3 day 3 mouse 1 feces |
| Sample type |
SRA |
| |
|
| Source name |
Yeast cells grown on Sabouraud plates
|
| Organism |
Candida albicans |
| Characteristics |
background strain: SN152
selection: mouse GI tract
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Phenol chloroform DNA extraction protocol
Fully described in STAR methods of Witchley, Penumetcha et al. 2018
LAM-PCR mediated deep-sequencing
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
growth in murine GI tract 3 days followed by plating to Sabouraud dextrose agar 2 days 30C
GI_Screen_3.xlsx
|
| Data processing |
Base calls performed by Illumina HiSeq 2500 platfom
Reads aligned to Candida genome using bowtie with default parameters
Maximum read count within 200 bp of start or end of each ORF reported
Gene lists filtered to only the genes included in the knockout collections screened
Each column divided by the total number of reads for that column to generate fractional abundance
Genes in knockout collection with less than 100 reads present in screen inoculum were removed from further analysis as they were assumed to be absent from the inoculum pool
Fractional abundance values for each knockout in each mouse sample was divided by the fractional abundance of the assciated screen inoculum
All ratios were log base 2 transformed
Genome_build: Candida albicans SC5314 Assembly 21
Supplementary_files_format_and_content: GI_Screen_1-3 contain log base 2 fold changes of each mutant abundance recovered from the mouse compared to the inoculum
|
| |
|
| Submission date |
Dec 19, 2018 |
| Last update date |
Dec 31, 2018 |
| 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 |
GPL19036 |
| Series (1) |
| GSE124139 |
Screens of C. albicans deletion collections in the murine reveals role for filamentation transcription factors |
|
| Relations |
| BioSample |
SAMN10616405 |
| SRA |
SRX5165692 |
