|
| Status |
Public on Mar 21, 2019 |
| Title |
WT-s |
| Sample type |
SRA |
| |
|
| Source name |
wild type
|
| Organism |
Salmonella enterica subsp. enterica serovar Typhimurium str. ATCC 14028 |
| Characteristics |
genotype/variation: wild type
growth phase: early-stationary
|
| Growth protocol |
Luria Broth at 37 degrees up to mid-log or stationary phase
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared using the RNAprotect Bacteria Reagent and RNeasy Protect Bacteria Kit (Qiagen, Valencia, CA, USA) according to the user’s manuals.
Standard protocol by Genewiz
Strand-specific RNA library preparation with rRNA depletion
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
WTs vs SDs comparisons.csv
|
| Data processing |
High-throughput RNA sequencing data were preprocessed for alignment with Cutadapt(64) to remove Illumina sequencing adapters and low-quality bases (PHRED<20) from the ends of reads.
Trimmed read pairs were then aligned to the NCBI GenBank assembly GCA_000022165.1 for S. enterica serovar Typhimurium 14028 using Bowtie2, and the resulting SAM files were converted to BAM files using SAMtools.
Aligned reads were quantified to individual genes in the annotated genome using Cufflinks and differential expression analysis among samples was performed with Cuffdiff using multi-read correction and FPKM library normalization.
|
| |
|
| Submission date |
Nov 30, 2018 |
| Last update date |
Mar 21, 2019 |
| Contact name |
Jiqiang Ling |
| E-mail(s) |
[email protected]
|
| Phone |
3014051035
|
| Organization name |
The University of Maryland, College Park
|
| Department |
Cell Biology and Molecular Genetics
|
| Lab |
Ling Lab
|
| Street address |
2202 Microbiology Bldg., 4062 Campus Dr.
|
| City |
College Park |
| State/province |
MD |
| ZIP/Postal code |
20742 |
| Country |
USA |
| |
|
| Platform ID |
GPL20792 |
| Series (1) |
| GSE123195 |
RNA-seq of Salmonlella Typhimurium variants |
|
| Relations |
| BioSample |
SAMN10506475 |
| SRA |
SRX5086136 |
