|
| Status |
Public on Aug 28, 2020 |
| Title |
CD630_WT1-Cy5_sig541-cy3 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
strain C630E grown 6h in TY (reference)
|
| Organism |
Clostridioides difficile |
| Characteristics |
strain: C630E Mullany
|
| Growth protocol |
C. difficile strain C630E was grown for 6 hours in TY medium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using phenol, Trizol reagent and chloroform/isoamylalcohol.
|
| 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 800 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 |
sig54 mutant grown 6h in TY
|
| Organism |
Clostridioides difficile |
| Characteristics |
strain: sigH::erm
|
| Growth protocol |
C. difficile strain C630E was grown for 6 hours in TY medium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using phenol, Trizol reagent and chloroform/isoamylalcohol.
|
| 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 800 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 Pro 6 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 |
Apr 23, 2020 |
| Last update date |
Aug 28, 2020 |
| Contact name |
Monot Marc |
| E-mail(s) |
mmonot@pasteur.fr
|
| 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 (1) |
| GSE149245 |
Comparison of the expression profiles of 630E strain and a sig54 mutant after 6h of growth |
|
