|
| Status |
Public on Jul 16, 2018 |
| Title |
55.St. Olav164 .IND.HUS |
| Sample type |
SRA |
| |
|
| Source name |
E. coli strain St. Olav164
|
| Organism |
Escherichia coli |
| Characteristics |
strain: St. Olav164
group (hus/non-hus): HUS
induced/non-induced: Induced
genome accession: PVRW00000000
|
| Treatment protocol |
The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C.
|
| Growth protocol |
Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre).
Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings
Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count
Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor).
Lowly expressed genes (<1 read per million) were removed.
Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor)
Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method
A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant
Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files
|
| |
|
| Submission date |
Mar 28, 2018 |
| Last update date |
Jul 16, 2018 |
| Contact name |
Christina Gabrielsen Aas |
| E-mail(s) |
christina.gabrielsen@stolav.no
|
| Organization name |
St. Olavs University Hospital
|
| Department |
Dept. of Medical Microbiology
|
| Street address |
Erling Skjalgssons gt 1
|
| City |
Trondheim |
| ZIP/Postal code |
7030 |
| Country |
Norway |
| |
|
| Platform ID |
GPL18133 |
| Series (1) |
| GSE112430 |
Comparative Transcriptome Profiling Reveals a Potential Role of Type VI Secretion System and Fimbriae in Virulence of Non-O157 Shiga Toxin-Producing Escherichia coli |
|
| Relations |
| BioSample |
SAMN08804800 |
| SRA |
SRX3856460 |
