|
| Status |
Public on Feb 05, 2019 |
| Title |
ST_22: RPF csrA:: 2 mLPM |
| 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: mLPM
|
| Treatment protocol |
Samples were treated with 100ug/ml choramphenicol for 2 minutes, quick chilled on ice, washed, and frozen with liquid nitrogen
|
| 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 |
Cell pellets were thawed, lysed with bead beating, and treated with micrococcal nuclease to release single monosomes. Ribosomes were isolated by ultracentrifuging lysate over a sucrose cushion. Ribosome protected fragments (RPF) were extracted from the pelleted ribosomes with miRNeasy RNA Extraction Kit (Qiagen) and size selected between 20 and 35 bases with denaturing PAGE.
RNA samples were ligated to a 3' adaptor and reverse transcribed. The cDNA was circularized to add a 5' adaptor then PCR amplified to add sample specific barcodes.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
ST_22
|
| Data processing |
Library strategy: ribosome profiling
Basecalls were made with Casava…
Reads were trimmed to remove adaptor sequences and reads shorter than 12 bases were discarded. Reads were aligned to the E. coli rRNA sequences with bowtie with default parameters and unaligned reads were retained
Reads were aligned to the Salmonella Typhimurium genome and plasmid sequences with bowtie using default parameters.
Read counts per gene were calculated with Htseq Count
Genome_build: NC_016855.1
Genome_build: NC_016856.1
Supplementary_files_format_and_content: Raw 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) |
| GSE107834 |
Analysis of the contribution of the post-transcriptional regulator CsrA to translation during exponential growth in Escherichia coli |
|
| Relations |
| BioSample |
SAMN08146589 |
| SRA |
SRX3456049 |
