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Status |
Public on Jul 16, 2018 |
Title |
42.St. Olav179.IND.nHUS |
Sample type |
SRA |
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Source name |
E. coli strain St. Olav179
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Organism |
Escherichia coli |
Characteristics |
strain: St. Olav179 group (hus/non-hus): Non-HUS induced/non-induced: Induced genome accession: GCA_000965705
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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.
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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.
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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).
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
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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
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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 |
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Relations |
BioSample |
SAMN08804747 |
SRA |
SRX3856447 |