|
| Status |
Public on Feb 05, 2019 |
| Title |
csrA LB T5 A |
| Sample type |
SRA |
| |
|
| Source name |
bacterial cells
|
| Organism |
Salmonella enterica subsp. enterica serovar Typhimurium |
| Characteristics |
strain: 14028s
genotype: csrA:: (markerless deletion of CDS after 51st codon)
medium: LB
time point: 5 min post-rifampicin addition
|
| Treatment protocol |
Samples were treated with 500ug/ml rifampicin and aliquoted collected at the indicated time points and added directly to a stop solution (5% phenol in ethanol). Samples were centrifuged and the stabilized RNA samples frozen at -80C until extraction.
|
| Growth protocol |
Strains were grown in LB (0.5% yeast extract, 1% NaCl, and 1% tryptone) or mLPM (0.5 uM ferric citrate, 5 mM KCl, 7.5 mM (NH4)2SO4, 0.5 mM K2SO4, 0.3% glycerol, 0.00001% thiamine, 337 uM KPO4, 80 mM MES pH 5.8, and 8 uM MgCl2) medium to mid-exponential phase (OD600 = 0.5 for LB and 0.3 for mLPM)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were extracted with hot phenol chloroform, treated with Turbo Dnase (Ambion), and cleaned with the RNeasy kit (Qiagen). RNA was normalized using fluorometric methods then an ERCC RNA spike-in was added to all samples (Ambion) to represent 5% of the total sample.
Standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
ST_13
|
| Data processing |
Basecalls were made with Casava
Reads were aligned to the Salmonella Typhimurium genome and plasmid sequences with bowtie2 using default parameters.
Read counts per gene were determined with Htseq Count
Reads within each time series were normalized to 4 independently collected qRT-PCR decay data for 11 genes
Genome_build: NC_016855.1
Genome_build: NC_016856.1
Supplementary_files_format_and_content: Normalized count matrix
|
| |
|
| Submission date |
Dec 07, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Anastasia Haley Potts |
| E-mail(s) |
anastasi@ufl.edu
|
| Organization name |
University of Florida
|
| Department |
Department of Microbiology and Cell Science
|
| Lab |
Dr. Tony Romeo
|
| Street address |
1355 Museum Drive, Bldg. 981
|
| City |
Gainesville |
| State/province |
FL |
| ZIP/Postal code |
32611 |
| Country |
USA |
| |
|
| Platform ID |
GPL17070 |
| Series (1) |
| GSE107835 |
Analysis of the contribution of the post-transcriptional regulator CsrA to RNA stability in Salmonella during growth in LB and mLPM media |
|
| Relations |
| BioSample |
SAMN08146626 |
| SRA |
SRX3456072 |
