|
| Status |
Public on May 27, 2015 |
| Title |
Ellermeier C difficile Iron fur rep1 tech1 |
| Sample type |
RNA |
| |
|
| Source name |
Clostridium difficile CD630 JIR8094 fur mutant
|
| Organism |
Clostridioides difficile 630 |
| Characteristics |
genotype: fur::ltrB::ermB
phenotype: fur-
accession: NC_003228 + NC_006873
|
| Growth protocol |
Clostridium difficile 630 erm wild type and fur mutant were grown to mid-log phase (O.D.600 nm 0.8) anerobically (80% N2, 10% CO2, 10% H2) at 37°C in tryptone-yeast extract medium containing 0.25 mM ferric chloride (Ho et al. Infect. Immun. ).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using trizol (Invitrogen) and contaminating DNA was removed by turbo DNase (Ambion) digestion. DNAseI was removed from the RNA samples using the RNeasy kit (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Genomics Division at the Iowa Institute of Human Genetics (University of Iowa, Iowa City, Iowa).
|
| Label |
Cy3
|
| Label protocol |
Labeling was performed by NimbleGen Inc., following their standard operating protocol. See www.nimblegen.com.
|
| |
|
| Hybridization protocol |
Hybridization was performed by NimbleGen Inc., following their standard operating protocol. See www.nimblegen.com.
|
| Scan protocol |
Scanning was performed by Roche NimbleGen, Inc., following their standard operating protocol. See www.nimblegen.com.
|
| Description |
This sample is of the Clostridium difficile CD630 JIR8094 fur::ltrB::erm mutant. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.
|
| 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 |
May 26, 2015 |
| Last update date |
May 27, 2015 |
| Contact name |
Craig D. Ellermeier |
| E-mail(s) |
[email protected]
|
| Phone |
319-384-4565
|
| Organization name |
University of Iowa
|
| Department |
Microbiology
|
| Street address |
51 Newton Rd 3-630 BSB
|
| City |
Iowa City |
| State/province |
IA |
| ZIP/Postal code |
52242 |
| Country |
USA |
| |
|
| Platform ID |
GPL20243 |
| Series (1) |
| GSE69218 |
Expression analysis of Clostridium difficile wild type and fur (ferric uptake regulator) mutant in high iron. |
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