|
| Status |
Public on Sep 28, 2017 |
| Title |
RPMI_liquid_37_a |
| Sample type |
SRA |
| |
|
| Source name |
RPMI_liquid_37
|
| Organism |
Candida albicans |
| Characteristics |
strain: SC5314
media substrate: liquid
temperature: 37
|
| Growth protocol |
SC5314 cells were grown overnight in YPD media at 30˚C with shaking. Cells were washed twice and resuspended with equal volumes of PBS. Cells were added to liquid or solid media as described below.
100 µl of washed cells were incubated in 50 ml of pre-warmed media in a 250 ml flask. Cells grown at 37˚C in liquid RPMI-MOPS with shaking for 3 hours
|
| Extracted molecule |
total RNA |
| Extraction protocol |
cell harvesting: Cells were harvested by filtration and then frozen at -80˚C.
RNA was collected from frozen cell pellets using the RNeasy kit (Qiagen) with minor modifications. Cell pellets were resuspended in the supplied resuspension buffer with 10 µl/ml beta-mecaptoethanol and moved to a 2 ml screw-cap tube. Cells were mechanically disrupted using 450 nm glass beads in a mini-bead beater (RPI), with three 1-minute bead beating pulses and 2 minute rests. The resulting supernatant was cleared of cell debris and RNA was precipitated with 70% EtOH. The cell supernatant/EtOH mix was placed into the purification column, washed, and eluted with 100 µl nuclease-free water. Residual genomic DNA was removed from the RNA samples during washing using a Qiagen RNase-free DNase on-column removal kit.
RNASeq libraries were generated beginning with 1.8 ng of total RNA following standardized protocols with the TruSeq RNA v2 kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
RPMI_L.txt
|
| Data processing |
All eight Candida chromosomes were downloaded from NCBI, and annotation was downloaded into a gff3 file, and transformed into a gtf file using gffread
Fastq files were generated using the bcl2fastq software, version 1.8.4. The fastq files for each sample were analyzed using the Tuxedo pipeline in order to find differentially expressed genes.
Read alignment was performed using tophat version 2.0. FPKM values were calculated with cufflinks 2.2.
Genome_build: ASM18296v3
Supplementary_files_format_and_content: tab-delimited text files include average FPKM values for each Sample. Average is across replicates.
|
| |
|
| Submission date |
Jun 11, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jill R Blankenship |
| E-mail(s) |
jrblankenship@unomaha.edu
|
| Organization name |
University of Nebraska at Omaha
|
| Department |
Biology
|
| Street address |
6001 Dodge St, AH114
|
| City |
Omaha |
| State/province |
NE |
| ZIP/Postal code |
68182 |
| Country |
USA |
| |
|
| Platform ID |
GPL19036 |
| Series (1) |
| GSE99902 |
Filamentation involves two overlapping, but distinct, programs of filamentation in the pathogenic fungus Candida albicans |
|
| Relations |
| BioSample |
SAMN07211907 |
| SRA |
SRX2901462 |
