|
| Status |
Public on Jul 15, 2014 |
| Title |
Hfq3-cy3_WT3-cy5 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Hfq antisense grown 7.5h Tyt
|
| Organism |
Clostridioides difficile |
| Characteristics |
strain/background: C630E Mullany Hfq antisense
genotype/variation: Hfq antisense
|
| Growth protocol |
C. difficile strain C630E and Hfq antisense strains were grown in Tyt.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using QIAgen RNeasy kit.
|
| 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.
|
| |
|
| Channel 2 |
| Source name |
630E strain grown 7.5h in Tyt (reference)
|
| Organism |
Clostridioides difficile |
| Characteristics |
strain/background: C630E Mullany
genotype/variation: wild-type
|
| Growth protocol |
C. difficile strain C630E and Hfq antisense strains were grown in Tyt.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using QIAgen RNeasy kit.
|
| 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.
|
| |
|
| |
| 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 a GenePix Pro 6 dual-channel laser scanner.
|
| Description |
Biological replicate 3 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 |
Feb 21, 2014 |
| Last update date |
Jul 15, 2014 |
| 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 |
GPL18319 |
| Series (2) |
| GSE55273 |
Comparison of the expression profiles of 630E strain and an Hfq antisense after 7.5h of growth in Tyt |
| GSE55274 |
Comparison of the expression profiles of 630E strain and hfQ mutants |
|
