|
| Status |
Public on Mar 20, 2024 |
| Title |
∆codY 24 hr biol rep 4 |
| Sample type |
SRA |
| |
|
| Source name |
early stationary phase
|
| Organism |
Bacillus subtilis |
| Characteristics |
tissue: early stationary phase
source: B. subtilis 168 genome (Gene Bank: NC_000964.3)
genotype: [delta]codY
time point: 24 hr
|
| Growth protocol |
Wild-type and ∆codY strains were grown to early stationary phase and inoculated on GYM7 plates with and without 1 µM chlormphenicol followed by incubation at 30℃ for 6 and 24 hours.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using TRI reagent and Turbo DNA-free kits.
RNA libraries for RNA-seq were prepared using the TruSeq Stranded mRNA kit per manufacturer's prtocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
DESeq2_codY24.csv
|
| Data processing |
RNAlysis V3.7.0
Sequences reads were trimmed for adaptor sequences with CutAdapt.
Trimmed sequence reads were mapped to open reading frames (ORFs) in the B. subtilis 168 genome (Gene Bank: NC_000964.3) plus sfp, swrA and ORFs in the plasmid pSB32 and then quantified with Kallisto (V0.48.0)
Normalized abundance of the reads was measured using DESeq2.
Assembly: B. subtilis 168 genome (Gene Bank: NC_000964.3) plus sfp, swrA and ORFs in the plasmid pSB32
Supplementary files format and content: comma separated file includes normalized abundance measurements via DESeq
|
| |
|
| Submission date |
Mar 19, 2024 |
| Last update date |
Mar 20, 2024 |
| Contact name |
Paul Straight |
| Organization name |
Texas A&M University
|
| Street address |
2128 TAMU
|
| City |
College Station |
| State/province |
TX |
| ZIP/Postal code |
77843 |
| Country |
USA |
| |
|
| Platform ID |
GPL19910 |
| Series (1) |
| GSE261934 |
Antibiotic Exposure Reprograms Metabolism to Mobilize Bacillus subtilis in competitive interactions |
|
| Relations |
| BioSample |
SAMN40546411 |
| SRA |
SRX23994466 |
