|
| Status |
Public on Oct 02, 2012 |
| Title |
ccpA_TY1-cy3 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Mutant ccpA CD630E JIR8094 10H in TY
|
| Organism |
Clostridioides difficile |
| Characteristics |
strain: CD630E JIR8094
genotype: ccpA::erm
treatment: 10H in TY
|
| Growth protocol |
C.difficile strains CD630E JIR8094, a WT and a mutant ccpA strains, were grown for 10 hours in TY
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using RNAPro (FastPrep) and following MP 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 |
CD630E JIR8094 in TY 8H of growth (reference)
|
| Organism |
Clostridioides difficile |
| Characteristics |
strain: CD630E JIR8094
treatment: 8H in TY
|
| Growth protocol |
C.difficile strains CD630E JIR8094, a WT and a mutant ccpA strains, were grown for 10 hours in TY
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using RNAPro (FastPrep) and following MP 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 1 of 4.
|
| 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 BH.
|
| |
|
| Submission date |
Jan 12, 2012 |
| Last update date |
Oct 02, 2012 |
| 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 |
GPL10556 |
| Series (4)
|
| GSE35070 |
Comparison of the expression profiles of 630E JIR8094 strain and a ccpA mutant after 10h of growth in TY with 0.5% glucose. |
| GSE35071 |
Comparison of the expression profiles of 630E JIR8094 strain and a ccpA mutant after 10h of growth in TY. |
| GSE35073 |
Clostridium difficile mutant ccpA CD630E JIR8094: growth 10h with 0.5% glucose in TY vs growth 10h in TY |
| GSE35152 |
Comparison of the expression profiles of 630E JIR8094 strain and a ccpA mutant |
|
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