|
| Status |
Public on Jan 31, 2018 |
| Title |
OuJ_inf3 |
| Sample type |
SRA |
| |
|
| Source name |
Distal colonic tissues
|
| Organism |
Mus musculus |
| Characteristics |
strain: C3Ou
condition: Infected
age: 5 weeks
post-infection period: 9 days
genotype: WT
|
| Treatment protocol |
C. rodentium strain DBS100 was grown overnight in 3 ml of LB medium shaking at 37oC. Five-week-old female mice (three per group) were infected by oral gavage with 0.1 ml of LB medium containing 2.7 x 108 colony-forming units of bacteria
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Distal colons were harvested and snap frozen in liquid nitrogen for RNA extraction.
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 |
| |
|
| Data processing |
RNA quality was assessed by a Bioanalyzer
Trimming was done with the Trimmomatic software
filtered reads were aligned to the mm10 mouse genome assembly with the combination of the TopHat/Bowtie software
Genome_build: mm10
Supplementary_files_format_and_content: text files include raw counts for each sample
|
| |
|
| Submission date |
Jun 27, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Samantha Gruenheid |
| E-mail(s) |
samantha.gruenheid@mcgill.ca
|
| Phone |
(514) 398-2138
|
| Organization name |
McGill University
|
| Department |
Microbiology and Immunology
|
| Street address |
3649 Promenade Sir-William-Osler, Room 365
|
| City |
Montreal |
| State/province |
Quebec |
| ZIP/Postal code |
H3G 0B1 |
| Country |
Canada |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE100546 |
Defining the responses governing disease tolerance during Citrobacter rodentium infection of mice by deep RNA sequencing |
|
| Relations |
| BioSample |
SAMN07281163 |
| SRA |
SRX2960434 |
