|
| Status |
Public on Feb 14, 2018 |
| Title |
wild-type Bacillus anthracis Sterne replicate 2 |
| Sample type |
RNA |
| |
|
| Source name |
wild-type Bacillus anthracis Sterne
|
| Organism |
Bacillus anthracis str. Sterne |
| Characteristics |
genotype: wild-type
|
| Treatment protocol |
N/A
|
| Growth protocol |
Bacterial strains were grown to early log phase (O.D.600nm 0.4) aerobically at 37°C in Brain Heart Infusion media.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc). DNA was removed using the Turbo DNA-free kit following the rigorous protocol described in manufacturers instructions (Thermo Fisher Scientific). RNA was concentrated using the Zymo RNA Clean & Concentrator-5 kit (Zymo Research). RNA quality and concentration was determined on the AGilent Bioanalyzer and NanoDrop spectrophotometer. All samples passed QC metrics set forth by Roche NimbleGen.
|
| Label |
Cy3
|
| Label protocol |
Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
|
| |
|
| Hybridization protocol |
Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.
|
| Scan protocol |
Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
|
| Description |
This sample is of wild-type Bacillus anthracis Sterne. It is the second of three wild-type biological replicates used in this experiment, each from separate cultures.
WT2
|
| Data processing |
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).
|
| |
|
| Submission date |
Feb 01, 2017 |
| Last update date |
Feb 15, 2018 |
| Contact name |
Shauna McGillivray |
| E-mail(s) |
s.mcgillivray@tcu.edu
|
| Organization name |
TCU
|
| Department |
Biology
|
| Street address |
2800 S. University Dr
|
| City |
Fort Worth |
| State/province |
TX |
| ZIP/Postal code |
76129 |
| Country |
USA |
| |
|
| Platform ID |
GPL23020 |
| Series (1) |
| GSE94398 |
Expression analysis of Bacillus anthracis Sterne wild-type and deltaClpX mutant strains |
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