|
| Status |
Public on Jan 21, 2018 |
| Title |
SM1_A |
| Sample type |
SRA |
| |
|
| Source name |
yeast
|
| Organism |
Nakaseomyces glabratus |
| Characteristics |
fluconazole mic (mg/ml): 4
genotype/variation: parent clinical isolate
|
| Treatment protocol |
There was no treatment of cells beond the listed growth conditions
|
| Growth protocol |
Cultures were maintained on YPD agar plates. To initiate cultures, a single colony was used to inoculate a 2-ml culture of YPD liquid medium, and this culture was grown to saturation overnight at 30 degrees Celsius. An aliquot of the overnight cultures was then used to inoculate 20 ml YPD liquid culture to achieve a final OD(600)= 0.2. These cultures were then grown at 30 degrees Celsius for 3 hours at which time cells were collected by centrifugation, supernatants removed, and cell pellets frozen at -80 degrees Celsius until RNA isolation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using the hot phenol method of RNA isolation. RNA concentrations were determined using a Nanodrop spectrophotometer, and RNA integrity was verified using a Bioanalyzer 2100.
Barcoded libraries were prepared using the Lexogen mRNA Sense kit for Ion Torrent according to the manufacturer's standard protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent PGM |
| |
|
| Description |
parent clinical isolate
|
| Data processing |
Individual sample fragments were concatenated to form the whole sample fastq file.
Files were run through FASTQC to check data quality. Any reads with a phred score<20 were trimmed.
Read counts for each sample were normalized using transcripts per kilobase million (TPM) method.
Genome_build: Reads were aligned to the C. glabrata CBS138 reference transcriptome using RNA-Star long method. Read counts for each sample were normalized using transcripts per kilobase million (TPM) method.
Supplementary_files_format_and_content: Processed data is in the form of an Excel matrix. Reads were aligned to the C. glabrata CBS138 reference genome for biological Samples A and B for the wild type and mutant strains. Normalized read counts aligned to each genomic feature are listed for each sample.
|
| |
|
| Submission date |
Oct 02, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Katherine S Barker |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Tennessee Health Science Center
|
| Department |
Clinical Pharmacy
|
| Lab |
David Rogers laboratory
|
| Street address |
881 Madison Avenue, Room 305
|
| City |
Memphis |
| State/province |
TN |
| ZIP/Postal code |
38163 |
| Country |
USA |
| |
|
| Platform ID |
GPL24070 |
| Series (1) |
| GSE104476 |
Transcriptional profiling of putative J protein Jjj1 in Candida glabrata |
|
| Relations |
| BioSample |
SAMN07728389 |
| SRA |
SRX3236431 |
