|
| Status |
Public on Mar 02, 2022 |
| Title |
2 |
| Sample type |
SRA |
| |
|
| Source name |
E-CIP-S2
|
| Organism |
Salmonella enterica subsp. enterica serovar Typhimurium |
| Characteristics |
evolved lins: Evolved clone
antibiotics treatment: no
plasmid-bearing: yes
|
| Treatment protocol |
In the absence of antibiotics
|
| Growth protocol |
RNA was extracted from clones cultured in LB broth after 4 h mating
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Bacterial cells were collected by 8000×g centrifugation for 10 min
The library was constructed using an Illumina TruSeq RNA sample Prep Kit v2
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Feb 25, 2022 |
| Last update date |
Mar 03, 2022 |
| Contact name |
Jinfei Zhang |
| E-mail(s) |
zjflinux@gmail.com
|
| Organization name |
SCAU
|
| Street address |
483 Wushan Road
|
| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510642 |
| Country |
China |
| |
|
| Platform ID |
GPL17070 |
| Series (1) |
| GSE197475 |
A trade-off for maintenance of multidrug-resistance IncHI2 plasmids in Salmonella Typhimurium through co-evolution |
|
| Relations |
| BioSample |
SAMN26263361 |
| SRA |
SRX14291557 |
