|
| Status |
Public on Mar 26, 2013 |
| Title |
sgrs_sgrt_mut_15 |
| Sample type |
SRA |
| |
|
| Source name |
Total RNA from bacterial cell culture
|
| Organism |
Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 |
| Characteristics |
growth phase: exponential growth
treatment: glucose-analog alpha-methyl glucoside
genotype: sgrs sgrt
strain: LT2
|
| Treatment protocol |
Each of the mutant strains above were grown in min. Mops fructose medium until cultures reached an OD600 of ~0.3. Cultures were then treated with the glucose-analog alpha-methyl glucoside (αMG), and total RNA harvested 15' after treatment
|
| Growth protocol |
Minimal mops medium , carbon source: fructose
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910.
Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper
Genome_build: Salmonella enterica subsp. Enterica serovar Typhimurium st. LT2 (NC_003197.1)/ASM694v1
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates.
|
| |
|
| Submission date |
Mar 23, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Brian Tjaden |
| Organization name |
Wellesley College
|
| Street address |
106 Central Street
|
| City |
Wellesley |
| State/province |
MA |
| ZIP/Postal code |
02481 |
| Country |
USA |
| |
|
| Platform ID |
GPL16864 |
| Series (1) |
| GSE45445 |
RNA-seq analysis of Salmonella enterica Typhimurium LT2 |
|
| Relations |
| SRA |
SRX254828 |
| BioSample |
SAMN01990905 |
