|
| Status |
Public on Nov 06, 2013 |
| Title |
CD630 Osmotic shock, replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
630_Brain heart infusion broth+1.5 % NaCl
|
| Organism |
Clostridioides difficile |
| Characteristics |
strain: 630
growth/treatment condition: exposed to Brain heart infusion broth supplimented with 1.5% NaCl for 1h
|
| Treatment protocol |
Bacteria were then collected by centrifugation at 2,000 x g for 5 minutes. These cells were then shifted to two physiologically relevant in vitro conditions. In the first condition, cells were subjected to nutrient change by shifting to an equal volume of Basal defined medium (BDM) with supplementation of 0.5% sucrose. In the second condition, cells were subjected to osmotic shock by shifting to an equal volume of BHI supplemented with 1.5% NaCl. The same number of cells was transferred to fresh BHI as the control group.
|
| Growth protocol |
Spores of C. difficile strains CD630, CD196, QCD_32g58 and R20291 were streaked on brain-heart infusion (BHI) agar plates containing 0.1% L-cysteine and taurocholate. The plates were incubated overnight at 37°C. Single colonies from these plates were then used inoculate pre-reduced BHI broth and were incubated at 37°C overnight. Fresh BHI broth was then inoculated by transferring 1% overnight culture. Cultures were incubated at 37°C until the OD600 reached between 0.4 - 0.5.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Groth was arrested by addition of twice volume of RNAprotect bacteria reagent. Cells were collected by centrifugation at 2,000 x g for 10 minutes. RNA was isolated using RNeasy kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
CD630-Salt-B
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
The quality of the raw sequence reads was checked using the FastQC program (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc). The processed reads were then aligned using Bowtie version 0.12.7 to the corresponding C. difficile reference genome. Read alignments with mapping quality score (MAPQ) < 10 were removed.
Cufflinks software package version 1.3.1 was used to assemble transcripts and estimate the relative abundances of the transcripts. Transcript expression levels are estimated as Fragments Per Kilobase per Million mapped reads (FPKM). Cuffdiff, a component of Cufflinks was used to calculate transcript expression levels. When compared to control condition, genes with log2 ratio ≥ 1.5 and FDR- adjusted p value less than or equal to 0.05 were considered as differentially expressed.
Genome_build: ASM920v1, ASM8522v1, ASM2710v1, ASM15266v1
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample.
|
| |
|
| Submission date |
Aug 30, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Joy Scaria |
| Organization name |
South Dakota State University
|
| Department |
Veterinary and Biomedical Sciences
|
| Street address |
SAR114
|
| City |
Brookings |
| State/province |
SD |
| ZIP/Postal code |
57007 |
| Country |
USA |
| |
|
| Platform ID |
GPL17666 |
| Series (1) |
| GSE50497 |
Differential stress transcriptome landscape of historic and recently emerged hypervirulent strains of Clostridium difficile strains determined using RNA-seq |
|
| Relations |
| BioSample |
SAMN02339988 |
| SRA |
SRX342226 |
