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| Status |
Public on Nov 06, 2013 |
| Title |
Differential stress transcriptome landscape of historic and recently emerged hypervirulent strains of Clostridium difficile strains determined using RNA-seq |
| Organism |
Clostridioides difficile |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose: To determine how divergent strains of C. difficile respond to environmental changes, the transcriptomes of two historic and two recently isolated hypervirulent strains were analyzed following nutrient shift and osmotic shock.
Methods: Following nutrient shift and osmotic shock, mRNA profile were determined using sequing of transcriptome in biological duplicates, using Illumina Hi-seq 2000.
Results: After applying the quality control steps, for each sample, sequence reads were 90 nucleotides in length and the total number of reads per sample was ~ 26.6 million on average. Expression of more than 90% CDS was detected under the three experimental conditions combined. About 20% of these genes were indentified to be differentially expressed at 1.5 fold or more.
Conclusions: Our results reveal that although C. difficile strains contain a large number of shared and strain specific genes, the majority of the differentially expressed genes were core genes. We also detected a number of transcriptionally active regions that were not part of the primary genome annotation. Some of these are likely to be small regulatory RNAs.
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| Overall design |
Differential stress transcriptomes of two historic (strain 630 and 196) and two recently emerged hypervirulent strains (stain R20291 and 32g58) of C. difficile was determined by deep sequencing, in duplicate, using Illumina Hi-Seq 2000.
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| Contributor(s) |
Scaria J, Chen J, Chunhong M, Chang Y |
| Citation(s) |
24244315 |
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| Submission date |
Aug 30, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Joy Scaria |
| Organization name |
South Dakota State University
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| Department |
Veterinary and Biomedical Sciences
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| Street address |
SAR114
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| City |
Brookings |
| State/province |
SD |
| ZIP/Postal code |
57007 |
| Country |
USA |
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| Platforms (1) |
| GPL17666 |
Illumina HiSeq 2000 ([Clostridium] difficile) |
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| Samples (24)
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| GSM1220193 |
CD630 Osmotic shock, replicate 2 |
| GSM1220194 |
CD630 Nutrient shift, replicate 1 |
| GSM1220195 |
CD630 Nutrient shift, replicate 2 |
| GSM1220196 |
CD196 Control, replicate 1 |
| GSM1220197 |
CD196 Control, replicate 2 |
| GSM1220198 |
CD196 Osmotic shock, replicate 1 |
| GSM1220199 |
CD196 Osmotic shock, replicate 2 |
| GSM1220200 |
CD196 Nutrient shift, replicate 1 |
| GSM1220201 |
CD196 Nutrient shift, replicate 2 |
| GSM1220202 |
R20291 Control, replicate 1 |
| GSM1220203 |
R20291 Control, replicate 2 |
| GSM1220204 |
R20291 Osmotic shock, replicate 1 |
| GSM1220205 |
R20291 Osmotic shock, replicate 2 |
| GSM1220206 |
R20291 Nutrient shift, replicate 1 |
| GSM1220207 |
R20291 Nutrient shift, replicate 2 |
| GSM1220208 |
32g58 Control, replicate 1 |
| GSM1220209 |
32g58 Control, replicate 2 |
| GSM1220210 |
32g58 Osmotic shock, replicate 1 |
| GSM1220211 |
32g58 Osmotic shock, replicate 2 |
| GSM1220212 |
32g58 Nutrient shift, replicate 1 |
| GSM1220213 |
32g58 Nutrient shift, replicate 2 |
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| Relations |
| BioProject |
PRJNA217778 |
| SRA |
SRP029366 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE50497_RAW.tar |
1.4 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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