|
| Status |
Public on Sep 17, 2016 |
| Title |
LT2, Tomato Shoot rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Bacterial cells grown on Tomato shoot
|
| Organism |
Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 |
| Characteristics |
strain: LT2
growth media: tomato shoot
|
| Growth protocol |
Salmonella cells were grown on either shoots or roots of tomato plants for 3 days until the cells were retrieved from the plants for mRNA isolation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tomato plants maintaining Salmonella cells were submerged in Qiagen RNAprotect solution to stabilize bacterial RNA. Total RNA was isolated from the bacterial cells dislodged from the plants using Qiagen RNeasy mini kit. The total RNA was depleted of prokaryotic ribosomal RNA using Epicentre Ribo-Zero rRNA removal kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1000 |
| |
|
| Data processing |
Illumina Casava v1.8.2 was used for basecalling.
Sequenced reads were trimmed of adaptor and barcode sequences using Trimmomatic (Bolger et al., 2014) with parameters ILLUMINACLIP:<adaptor.fasta>:2:30:10 HEADCROP:10 SLIDINGWINDOW:4:20 MINLEN:70, then mapped to S. Typhimurium LT2 whole genome (NC_003197 and NC_003277) using bowtie v2.1.0 and tophat v2.0.9 with tophat parameters --library-type=fr-firststrand.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using a protocol from Trapnell et al., Nature Protocols, 2012. In short, the reads and the merged assembly were fed to Cuffdiff which normalizes read counts into FPKM (fragments per kilobase of transcript per million mapped fragments), calculates expression levels, and tests the statistical significance of observed changes in expression levels.
Genome_build: NC_003197 and NC_003277
Supplementary_files_format_and_content: Tab-delimited files including averaged FPKM values for each condition.
|
| |
|
| Submission date |
Sep 18, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Sanghyun Han |
| E-mail(s) |
h.sanghyun@gmail.com
|
| Organization name |
RDA-NAAS
|
| Street address |
166 Nong-Saeng-Myung-Ro
|
| City |
Wan-Ju-Goon |
| ZIP/Postal code |
55365 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL20934 |
| Series (1) |
| GSE73192 |
Genome-Wide Transcriptional Profiling of Salmonella Typhimurium Epiphytically Colonizing Tomato Points to Anaerobic Respiration, and Nitrosative and Oxidative Stress Responses |
|
| Relations |
| BioSample |
SAMN04096035 |
| SRA |
SRX1258662 |
