|
| Status |
Public on Nov 06, 2018 |
| Title |
Sample_264UKLPM |
| Sample type |
SRA |
| |
|
| Source name |
poultry-associated field strains of S. Enteritidis grown in LPM media at avian body temperature (42C)
|
| Organism |
Salmonella enterica subsp. enterica serovar Enteritidis |
| Characteristics |
strain: UK
phenotype: High-pathogenic
|
| Treatment protocol |
No special treatment
|
| Growth protocol |
A single colony of an overnight culture was inoculated onto Luria Bertani broth (LB) and incubated at 42C for 16 hours and 200 rpm shaking. These overnight cultures were diluted 1:100 into LB-salt (300mM NaCl) or LPM broth and incubated at 42C for 4 hours with shaking at 180 rpm. Cell pellets were obtained for total RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction and DNAse treatment were performed with RiboPure Bacterial RNA Kit (Ambion, USA) following manufacter's instructions. For each strain in both conditions, a pool containing equimolar amounts of total RNA from 3 independent replicates was submitted for RNA-Seq.
Libraries were prepared by Illumina, Inc. (San Diego, CA) using TruSeq RNA sample Prep Kit following manufacturer's instructions (Illumina, Inc).
Libraries were sequenced on a HiSeq 2000 instrument using version 3 chemistry (75bp paired-end reads)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Cultured in LPM (low phosphate, low magnesium) at 42C
|
| Data processing |
Demultiplexing and base calling were performed using CASAVA 1.8
Casava 1.8-quality filtered reads were paired (QC>30), trimmed and aligned to S. Enteritidis strain P125109 reference sequence using Geneious V11.15 (Biomatters Ltd, New Zealand). Alignment was performed with a minimum of 65bp, allowing up to two mismatches and >90% of the each reads length had to map to the reference sequence to be considered as mapped reads.Read counts were adjusted to RPKM (Reads per kilobase per million).
Genes with zero reads were removed from analysis and total raw read counts were adjusted to RPKM values (Reads per kilobase per million) using Geneious V11.15. RPKM values below 10 were excluded from analysis.
Processed data files in txt format are summarized to include raw reads and RPKM values
Genome_build: NCBI: NC_011294
|
| |
|
| Submission date |
Nov 05, 2018 |
| Last update date |
Nov 06, 2018 |
| Contact name |
Devendra H Shah |
| E-mail(s) |
dshah@wsu.edu
|
| Phone |
509-335-6071
|
| Organization name |
Washington State University
|
| Department |
Veterinary Microbiology and Pathology
|
| Lab |
Shah Lab
|
| Street address |
#402, Bustad Hall
|
| City |
Pullman |
| State/province |
Washington |
| ZIP/Postal code |
99163 |
| Country |
USA |
| |
|
| Platform ID |
GPL17074 |
| Series (1) |
| GSE122177 |
Identification of common highly expressed genes of Salmonella Enteritidis by in silico prediction of gene expression and in vitro transcriptomic analysis |
|
| Relations |
| BioSample |
SAMN10380335 |
| SRA |
SRX4980134 |
