|
| Status |
Public on Aug 15, 2017 |
| Title |
E. coli 401140_DMEMB_0.5_BR2 |
| Sample type |
SRA |
| |
|
| Source name |
Escherichia coli cells
|
| Organism |
Escherichia coli 401140 |
| Characteristics |
strain: 401140
growth media: DMEMB
|
| Growth protocol |
The E. coli strains were grown overnight in LB media and were inoculated 1:100 into 250 ml of fresh LB or DMEM with bile (LBB and DMEMB) or without and were incubated with shaking (225 rpm) at 37˚C to a final optical density (OD600) of approximately 0.5.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from pelleted cells using the Ribopure Bacteria kit (Ambion) and contaminating DNA was removed using the Ribopure Dnase I and also the Turbo DNA-free kit (Ambion).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
401140_DMEMB_vs_LBB.txt,401140_DMEMB_vs_DMEM.txt
|
| Data processing |
Illumina reads were mapped to the EPEC genomes using Bowtie
The mapped reads were counted using HTSeq and normalized and then the differential expression of each gene for one sample compared to another was determined using DESeq v. 1.5.24, and statistical analyses were performed using R-2.15.2, and was represented as the log2 of the fold-change values.
Genome_build: E2348/69, HS, H10407, 102651, 102712, 401140, 402290
Supplementary_files_format_and_content: read count, FC, differential expression
|
| |
|
| Submission date |
Sep 09, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Sean Daugherty |
| E-mail(s) |
sdaugherty@som.umaryland.edu
|
| Phone |
410-706-8012
|
| Organization name |
University of Maryland School of Medicine
|
| Department |
Institute for Genome Sciences
|
| Street address |
801 W. Baltimore St.
|
| City |
Baltimore |
| State/province |
Maryland |
| ZIP/Postal code |
21201 |
| Country |
USA |
| |
|
| Platform ID |
GPL21006 |
| Series (2) |
| GSE86638 |
Comparative genomics and transcriptomics of Escherichia coli isolates carrying virulence factors of both enteropathogenic and enterotoxigenic Escherichia coli 401140 |
| GSE86640 |
Comparative genomics and transcriptomics of Escherichia coli isolates carrying virulence factors of both enteropathogenic and enterotoxigenic Escherichia coli |
|
| Relations |
| BioSample |
SAMN02679959 |
| SRA |
SRX483623 |
