|
| Status |
Public on Sep 27, 2020 |
| Title |
C. difficile R20291 rough-rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
C. difficile R20291
|
| Organism |
Clostridioides difficile R20291 |
| Characteristics |
tissue: bacterial culture
isolate: rough colony isolate
culture: grown on BHIS-agar
|
| Growth protocol |
All steps anaerobic, 37 degrees C. Grown from freezer stocks on BHIS-agar, overnight incubation. Strain passaged on BHIS-agar, overnight incubation. Individual rough or smooth coloniy was grown overnight (14-16h) in BHIS broth. Culture (5uL) was spotted onto BHIS-agar and incubated for 24 hours.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Growth was collected from plates and suspended in 1:1 ethanol:acetone. Cell pellets collected by centrifugation. RNA extraction with TriSure and chloroform, beadbeating, and isopropanol/ethanol precipitation. Quality verified with Bioanalyzer Assay.
Ribozero rRNA Removal Kit, NEBNext Ultra RNA Library Prep Kit for Illumina, Illumina HiSeq 2500 instrument
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
HiSeq Control Software was used for basecalling. Raw sequence data files (.bcl) were converted the FASTQ format and de-multiplexed with bcl2fastq 2.17 software (Illumina). One mismatch was permitted for index sequence identification.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to C. difficile R20291 whole genome in CLC Genomics Workbench v20. Default settings for RNA-seq were used (allows 1 mismatch per read)
Reads Per Kilobase per Megabase of library size (RPKM) were calculated using CLC Genomics Workbench v20
Genome_build: C. difficile R20291 reference genome, FN545816
Supplementary_files_format_and_content: Excel spreadsheet containing read information for individual samples (sheet 1), differential expression analysis (sheet 2), and list of genes >2-fold changed and p < 0.05 (sheet 3) with FDR correction
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample
|
| |
|
| Submission date |
Sep 18, 2020 |
| Last update date |
Sep 28, 2020 |
| Contact name |
Rita Tamayo |
| E-mail(s) |
rita_tamayo@med.unc.edu
|
| Organization name |
University of North Carolina at Chapel Hill
|
| Department |
Microbiology and Immunology
|
| Lab |
Tamayo
|
| Street address |
125 Mason Farm Rd, CB# 7290
|
| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599 |
| Country |
USA |
| |
|
| Platform ID |
GPL24374 |
| Series (1) |
| GSE158225 |
Differentially expressed genes in rough and smooth colony isolates of Clostridioides difficile |
|
| Relations |
| BioSample |
SAMN16212691 |
| SRA |
SRX9152015 |
