|
| Status |
Public on Jun 01, 2021 |
| Title |
as-ssn3 + 3-MB-PP1 3h rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
single species liquid culture
|
| Organism |
Candida albicans |
| Characteristics |
strain: SC5314
genotype: ssn3-AS
treatment: 3-MB=PP1
time point (hours): 3
|
| Treatment protocol |
3-MB-PP1 was added 5 minutes prior to transfter to hypha-formation permissive medium.
|
| Growth protocol |
C. albicans ssn3-AS was grown as a YPD for 16 hours at 30℃, washed once, then inoculated into room temperature YNB medium.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cell pellets were dissolved in Trizol and cells were lysed by bead beating. Lysate was phase separated by centrifugation and from the aqueous phase RNA was precipitated by linear acrylimide. Centrifugation collected the RNA into a pellet that was, after supernatent removal, washed with ethanol and resuspended into deionized, nuclease-free water.
RNA was treated with Dnase using the Rneasy MinElute protocol and ribo-depletion using RiboZero (bacteria). Library prep was done as the Illumina TrueSeq Stranded RNAseq.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
JH20
|
| Data processing |
Basecalls - Illumina native app
Trimming - Illumina native app to trim adapter sequences
Quality Control CLC Genomics Workbench: quality score = 0.05, ambiguous bases = 2, auto adapter trim = NO, trim bases 5' and 3', filter length above = NO, filter length below = NO
Allignment to Ca genome - CLC Workbench: mismatched cost = 2, insertion cost = 2, deletion cost = 3, length fraction = 0.8, similarity fraction = 0.8, strands = both, max # hits per read = 10, global allignment = NO
CGD Assembly22
Supplementary_files_format_and_content: Counts per million (CPM) for all samples in a .csv file
|
| |
|
| Submission date |
Apr 11, 2021 |
| Last update date |
Jun 01, 2021 |
| Contact name |
Deborah Ann Hogan |
| E-mail(s) |
DHOGAN@DARTMOUTH.EDU
|
| Phone |
603-650-1252
|
| Organization name |
Geisel School of Medicine
|
| Department |
Microbiology and Immunology
|
| Street address |
HB7550
|
| City |
Hanover |
| State/province |
NH |
| ZIP/Postal code |
03755 |
| Country |
USA |
| |
|
| Platform ID |
GPL22403 |
| Series (1) |
| GSE171859 |
Transcriptional profiling analysis of the effects of Ssn3 inhibition in Candida albicans |
|
| Relations |
| BioSample |
SAMN18710726 |
| SRA |
SRX10575787 |
