|
| Status |
Public on Sep 25, 2019 |
| Title |
D1.cpxR1biofilm |
| Sample type |
SRA |
| |
|
| Source name |
Bacterial cells
|
| Organism |
Salmonella enterica subsp. enterica serovar Enteritidis |
| Characteristics |
genotype: Isogenic cpxR mutant
growth phase: Biofilm
|
| Treatment protocol |
Approximately 100 million colony-forming units of the wild-type and cpxR planktonic cells and biofilm were centrifuged at 1844 x g for 10 min. All bacterial samples were re-suspended in RNAprotect bacterial agent (Qiagen, Valencia, CA, USA) and stored at -20°C until RNA extraction
|
| Growth protocol |
Planktonic cells were harvested during the mid log growth phase, while biofilm samples were harvested after a two-day growth period.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the RNAeasy Kit from Qiagen
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Raw sequence that passed CASAV 1.8P/F filter were assessed by fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Read mapping was performed via Hisat2 (v2.0.2) using the Salmonella eneterica serovar Enteritidis str. P125109 as reference.
Cuffdiff 2.2.1 was used to quantify the expression level of each known gene in units of FPKM (fragment mapped per kilobase of exons per million mapped reads)
Differentially expressed genes were identified using the edgeR (negative binomial) feature in CLCGWB (Qiagen, Redwood city, CA) using raw read counts.
Genome_build: Salmonella enterica subsp. enterica serovar Enteritidis str. P125109 (Taxonomy ID: 550537)
Supplementary_files_format_and_content: raw read count
|
| |
|
| Submission date |
Sep 24, 2019 |
| Last update date |
Sep 26, 2019 |
| Contact name |
Sinisa Vidovic |
| E-mail(s) |
svidovic@umn.edu
|
| Phone |
6126263669
|
| Organization name |
University of Minnesota
|
| Street address |
1971 Commonwealth Avenue
|
| City |
Saint Paul |
| State/province |
MN |
| ZIP/Postal code |
55108 |
| Country |
USA |
| |
|
| Platform ID |
GPL27515 |
| Series (1) |
| GSE137932 |
Role of CpxR in biofilm development: expression of key fimbrial, O-antigen and virulence operons of Salmonella Enteritidis |
|
| Relations |
| BioSample |
SAMN12830348 |
| SRA |
SRX6895318 |
