|
| Status |
Public on Feb 28, 2017 |
| Title |
DMSO_Sterne1 |
| Sample type |
SRA |
| |
|
| Source name |
Bacterial cells, DMSO
|
| Organism |
Bacillus anthracis str. Sterne |
| Characteristics |
strain/background: Sterne
treatment compound: DMSO
|
| Treatment protocol |
Samples were treated with 0.25X MIC compound (plantazolicin or Me2-Arg-Az5) or an equivalent volume of DMSO, and allowed to incubate for 10 min at 37 °C. Samples were treated with Qiagen RNAprotect bacterial reagent and harvested at 4000 x g for 10 min.
|
| Growth protocol |
(3) independent 3 mL cultures for each treatment group were grown to optical density (600 nm) of 0.4.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Harvested cells were resuspended in 250 μl of 10 mM Tris (pH 8.5) with 15 mg/ml lysozyme and 5 μl proteinase K (20 mg/ml) and digested for 1 h at 22°C with gentle agitation. RNA was extracted using the Qiagen RNeasy Mini Kit. An on-column DNase I digestion was performed using the Qiagen RNase-free DNase set according to manufacturer's instructions. RNA isolation protocol was completed according to manufacturer's instructions, followed by a second DNase I digestion and an RNA cleanup protocol.
Libraries were created using the TruSeq Stranded RNA Sample Prep kit after rRNA depletion using the RiboZero Bacteria kit, following manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Bacillus anthracis Sterne 7702
mRNA
Processed data file: NC_005945_transcripts_DMSO_PZN.txt
Processed data file: NC_005945_transcripts_DMSO_Az5.txt
|
| Data processing |
Data was processed with the Rockhopper version 1.30 pipeline using B. anthracis Sterne (NC_005945.1) and B. anthracis Ames Ancestor plasmid pXO1 (NC_007322.2) as references.
Default values (allowed mismatches 0.15, minimum seed length 0.33, minimum expression of UTRs and ncRNAs 0.5) were used, with the exception that reverse complement reads were used for mapping.
Genome_build: B. anthracis Sterne: NC_005945.1
Genome_build: B. anthracis Ames Ancestor plasmid pXO1: NC_007322.2
Supplementary_files_format_and_content: Tab-delimited text files include expression values that are counts normalized using the Rockhopper pipeline.
|
| |
|
| Submission date |
Sep 22, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Douglas A Mitchell |
| E-mail(s) |
douglasm@illinois.edu
|
| Phone |
2173331345
|
| Organization name |
University of Illinois at Urbana-Champaign
|
| Department |
Chemistry
|
| Lab |
Mitchell Lab
|
| Street address |
1206 W. Gregory Dr. MC-195 Room 3105 IGB
|
| City |
Urbana |
| State/province |
IL |
| ZIP/Postal code |
61801 |
| Country |
USA |
| |
|
| Platform ID |
GPL20947 |
| Series (1) |
| GSE73343 |
Bacillus anthracis gene expression upon plantazolicin and Me2-Arg-Az5 |
|
| Relations |
| BioSample |
SAMN04102791 |
| SRA |
SRX1275041 |
