|
| Status |
Public on Aug 02, 2014 |
| Title |
Slide2.3 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
wt_hpi_12
|
| Organism |
Clostridioides difficile |
| Characteristics |
strain: wild type
time point: hpi_12
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Trizol following manufacturer's instructions
|
| Label |
cy3
|
| Label protocol |
6 µg of total RNA were primed with 2 µl (1.6 µg/µl) random nanomers at 70°C for 5 min, then reversed transcribed at 42°C for 16 h in the presence SuperScript III RTase (life technologies), and 25X AA-dUTP/nucleotide mix. Synthesized cDNA was labeled with DyLight550 or DyLight650
|
| |
|
| Channel 2 |
| Source name |
CD3284_hpi_12
|
| Organism |
Clostridioides difficile |
| Characteristics |
strain: CD3284
wild type: hpi_12
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Trizol following manufacturer's instructions
|
| Label |
cy5
|
| Label protocol |
6 µg of total RNA were primed with 2 µl (1.6 µg/µl) random nanomers at 70°C for 5 min, then reversed transcribed at 42°C for 16 h in the presence SuperScript III RTase (life technologies), and 25X AA-dUTP/nucleotide mix. Synthesized cDNA was labeled with DyLight550 or DyLight650
|
| |
|
| |
| Hybridization protocol |
300 ng labeled cDNA (1:1 RATIO) were hybridized (2xgex Hi-RPM hybridisation buffer) for 17hr at 65 C and 10 rpm.
|
| Scan protocol |
Scanned on a GenePix scanner. Images were quantified using GenePix 6.1 software program.
|
| Data processing |
LiimaR package via Genome2D (http://genome 2d.molgenrug.nl), LOESS normalized, followed by quantile normalization between the slides
|
| |
|
| Submission date |
Mar 14, 2014 |
| Last update date |
Aug 03, 2014 |
| Contact name |
Jeroen Corver |
| E-mail(s) |
J.corver@lumc.nl
|
| Organization name |
LUMC
|
| Department |
Medical Microbiology
|
| Street address |
Albinusdreef 2
|
| City |
Leiden |
| ZIP/Postal code |
2333ZA |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL18424 |
| Series (1) |
| GSE55926 |
Transcriptional profiling of an HtrA proteases knock-out compared to wild type |
|
