|
| Status |
Public on Apr 01, 2021 |
| Title |
SC-BactRS-12S-SCR-346_S12_R1_001 |
| Sample type |
SRA |
| |
|
| Source name |
∆chvI chvI(D52E)++
|
| Organism |
Caulobacter vibrioides |
| Characteristics |
strain: CB15
genotype: delta_chvI xylX::pMT585-chvI(D52E)
|
| Growth protocol |
2 mL PYE cultures were inoculated with ∆chvI EV and ∆chvI chvI(D52E)++ cells and grown overnight. Cultures were diluted to OD660 = 0.001 in 2 mL fresh PYE and grown for 22.5 hours. Cultures were diluted to OD660 = 0.075 in 5 mL PYE + 0.15% xylose and grown for 3.5 hours before TRIzol extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from C. crescentus cell pellets using TRIzol per manufacturer protocol, followed by purification with a Qiagen RNeasy kit.
RNA-seq libraries were prepared using an Illumina TruSeq stranded RNA kit and sequenced on an Illumina NextSEQ500 instrument
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
FastQ files from Illumina NextSEQ500 were processed using the CLC genomics workbench (Qiagen) RNA-seq data analysis pipeline.
Reads were mapped to the coding regions of the Caulobacter crescentus NA1000 genome (accession CP001340)
Genome_build: GenBank accession CP001340
Supplementary_files_format_and_content: Processed files report the results of expression analysis in CLC Genomics Workbench in tab-delimited .txt format.
|
| |
|
| Submission date |
Mar 15, 2021 |
| Last update date |
Apr 02, 2021 |
| Contact name |
Sean Crosson |
| E-mail(s) |
crosson4@msu.edu
|
| Phone |
5178845345
|
| Organization name |
Michigan State University
|
| Department |
Dept. Microbiology and Molecular Genetics
|
| Street address |
567 Wilson Rd
|
| City |
East Lansing |
| State/province |
Michigan |
| ZIP/Postal code |
48824 |
| Country |
USA |
| |
|
| Platform ID |
GPL24555 |
| Series (1) |
| GSE168965 |
Defining the transcriptional regulon of ChvI in Caulobacter crescentus |
|
| Relations |
| BioSample |
SAMN18315627 |
| SRA |
SRX10348162 |
