|
| Status |
Public on Dec 31, 2013 |
| Title |
FliC2-WT2_Vivo |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
FliC mutant grown 14h in vivo
|
| Organism |
Clostridioides difficile |
| Characteristics |
strain background: R20291
genotype/variation: fliC::erm (fliC mutant)
|
| Growth protocol |
C.difficile strains R20291 strain : a wild type strain, a fliC mutant and a fliC mutant complemented after 14h of growth in PY and a wild type strain and a fliC mutant after 14h of mouse infection in Vivo
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using RNAPro Blue (FastPrep) and following Qbiogen manufacturer's instructions
|
| Label |
cy3
|
| Label protocol |
10 µg of total RNA and pdN6 primer were heated at 70°C for 5 min, then reversed transcribed at 42°C for 3 h in the presence of 1600 U SuperScript III Reverse Transcriptase (Invitrogen), each dATP, dTTP, dGTP, dCTP. cDNA were then incubated with cy5 or cy3 dyes 1h at room temperature in the dark.
|
| |
|
| Channel 2 |
| Source name |
R20291 grown 14h in PY (reference)
|
| Organism |
Clostridioides difficile |
| Characteristics |
strain background: R20291
genotype/variation: wild type
|
| Growth protocol |
C.difficile strains R20291 strain : a wild type strain, a fliC mutant and a fliC mutant complemented after 14h of growth in PY and a wild type strain and a fliC mutant after 14h of mouse infection in Vivo
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using RNAPro Blue (FastPrep) and following Qbiogen manufacturer's instructions
|
| Label |
cy5
|
| Label protocol |
10 µg of total RNA and pdN6 primer were heated at 70°C for 5 min, then reversed transcribed at 42°C for 3 h in the presence of 1600 U SuperScript III Reverse Transcriptase (Invitrogen), each dATP, dTTP, dGTP, dCTP. cDNA were then incubated with cy5 or cy3 dyes 1h at room temperature in the dark.
|
| |
|
| |
| Hybridization protocol |
samples were applied to microarrays enclosed in Agilent hybridization chambers for 17h at 65°C. After hybridization, slides were washed with Agilent washing buffers
|
| Scan protocol |
Scanned on an GenePix 4200L dual-channel laser scanner
|
| Description |
Biological replicate 3 of 3.
raw data file: F_FliC-02_cy3-400_cy5-350.gpr
|
| Data processing |
R limma package - Function used - Background correction : backgroundCorrect normexp ; Normalization : normalizeWithinArrays loess - Correlation of spot duplicat : duplicateCorrelation - Adjust to linear method : lmFit - Statistical analysis : eBayes, decideTests global BY [statistical results provided as Series Supplementary file].
|
| |
|
| Submission date |
Feb 10, 2012 |
| Last update date |
Dec 31, 2013 |
| Contact name |
Monot Marc |
| E-mail(s) |
[email protected]
|
| Phone |
+33145688390
|
| Organization name |
Institut Pasteur
|
| Department |
Genomes and Genetics
|
| Lab |
Biomics
|
| Street address |
25, rue du docteur roux
|
| City |
Paris |
| ZIP/Postal code |
75015 |
| Country |
France |
| |
|
| Platform ID |
GPL15218 |
| Series (1) |
| GSE35727 |
Comparison of the expression profiles of R20291 strain : a wild type strain, a fliC mutant and a fliC mutant complemented after 14h of growth in PY and a wild type strain and a fliC mutant after 14h of mouse infection in vivo |
|
