 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on May 31, 2019 |
| Title |
Cg_E_2_12h |
| Sample type |
SRA |
| |
|
| Source name |
Candida biofilms
|
| Organism |
Nakaseomyces glabratus |
| Characteristics |
cg strain: ATCC 2001
cg genotype: GFP labeled
culture condition: Cg monoculture
time: 12h
|
| Growth protocol |
Prior to the experiments, strains were cultured on Yeast Peptone Dextrose (YPD) agar plates for 48 hours at 30°C. For all experiments, single colonies were isolated from YPD agar plates and inoculated into 25 mL YNB medium (50 mM glucose and pH 7, Amresco). Cultures were grown overnight at 30°C and 170 rpm for 12 hours prior to experiments. Cultures were washed twice in PBS and adjusted to a cell density of ~10^7 cells/mL. A final volume of 4 mL was used per well. Biofilms were grown for 6, 12, and 24 hours on glass coverslips (pre-incubated in HI FBS) in 6-well tissue culture plates.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Biofilms were washed off of the coverslip with pre-chilled sterile MilliQ water and cells were collected by centrifugation (2000 x g, 5 minutes, 4 °C). Supernatant was removed and cell pellets were flash-frozen in liquid nitrogen prior to lyophilization for 24 hours. Acid-washed glass beads (Sigma-Aldrich) were added to the dried cell pellets and disrupted in the Disruptor Genie for 2 minute cycles for up to 10 minutes. Lysis buffer from the GE Illustra RNAspin Mini kit was added to the disrupted cell powder and RNA was extracted using the kit protocol with on-column DNase I treatment. RNA quality and concentration were determined using a Nanodrop® and Qubit™, respectively.
RNA libraries were constructed using TruSeqRNA kit and processed (125SE) on an Illumina HiSeq 2500 v4 High Output instrument
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Cg monoculture rep 2
|
| Data processing |
Illumina software used for base-calling
RNA-sequencing analysis was done using the Galaxy interface, through the Texas A&M High Performance Research Computing Center. In Galaxy, raw reads were trimmed of adapter sequences using Trimmomatic In Trimmomatic, TruSeq3 adapter sequences were used and selected operations were MINLEN (20), LEADING (3), TRAILING (3). MINLEN drops reads below a specified length (in this case 20 bp), and LEADING/TRAILING cuts off bases from the start/end of the read if the quality is below a certain threshold (set to default of 3).
Reads were mapped to the reference genome using Tophat2. In Tophat2, intron length was set to 10 – 1500 bp as previously described and all other parameters were set to default
After mapping, HTseq-counts was used to count how many reads mapped to each feature of the genome using the aligned sequencing reads and a list of genomic features as the input
The Bioconductor DEseq2 package was used to analyze HTseq-count data for differentially expressed genes
Genome_build: C_albicans_SC5314_version_A22-s07-m01-r06 (for *Ca_counts.xlsx files) and C_glabrata_CBS138_version_s02-m07-r08 (for *Cg_counts.xlsx files)
Supplementary_files_format_and_content: Excel format data sheets, raw count data for each file name/sample.
|
| |
|
| Submission date |
Aug 27, 2018 |
| Last update date |
May 31, 2019 |
| Contact name |
Katy Kao |
| E-mail(s) |
[email protected]
|
| Phone |
9798455571
|
| Organization name |
Texas A&M University
|
| Department |
Chemical Engineering
|
| Lab |
506/508
|
| Street address |
3122 TAMU Room 200
|
| City |
College Station |
| State/province |
Texas |
| ZIP/Postal code |
77843-3122 |
| Country |
USA |
| |
|
| Platform ID |
GPL25492 |
| Series (1) |
| GSE119059 |
Transcriptomic analysis of Candida albicans and Candida glabrata co-culture biofilms |
|
| Relations |
| BioSample |
SAMN09916032 |
| SRA |
SRX4613344 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3357216_2E_12_S66_L007_R1_001_Cg_counts.xlsx |
113.0 Kb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
