|
| Status |
Public on Jan 04, 2016 |
| Title |
pdf-1 KO vs. wild type 5889 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
1-N2 - 1
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: N2 wild type
stage: young adult
tissue: whole-mount
gender: hermaphrodite
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen mini kit
|
| Label |
Cy5
|
| Label protocol |
RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 1 µg of total RNA spiked with 10 viral polyA transcript controls (Agilent) was converted to double stranded cDNA in a reverse transcription reaction. Subsequently the sample was converted to antisense cRNA, amplified and labeled with Cyanine 5-CTP (Cy5) in an in vitro transcription reaction according to the manufacturer’s protocol (Agilent).
|
| |
|
| Channel 2 |
| Source name |
2-LSC0027- 1
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: LSC0027
stage: young adult
tissue: whole-mount
gender: hermaphrodite
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen mini kit
|
| Label |
Cy3
|
| Label protocol |
RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 1 µg of total RNA spiked with 10 viral polyA transcript controls (Agilent) was converted to double stranded cDNA in a reverse transcription reaction. Subsequently the sample was converted to antisense cRNA, amplified and labeled with Cyanine 3-CTP (Cy3) in an in vitro transcription reaction according to the manufacturer’s protocol (Agilent).
|
| |
|
| |
| Hybridization protocol |
A mixture of purified and labeled cRNA (Cy3 label: 14 pmol; Cy5 label: 10 pmol) was hybridised on Agilent C. elegans (V2) Gene Expression Microarray followed by (manual) washing, according to the manufacturer’s procedures.
|
| Scan protocol |
To assess the raw probe signal intensities, arrays were scanned using the Agilent DNA MicroArray Scanner with surescan High-Resolution Technology and probe signals were quantified using Agilent’s Feature Extraction software (version 9.5.3.1).
|
| Description |
hermaphrodite young adult sample
|
| Data processing |
The Agilent processed signal values (i.e., features gProcessedSignal and rProcessedSignal from Agilent Feature Extraction v9.5.3.1) were used for the data analysis. Base 2 log-ratios (Cy5/Cy3 intensities) were computed and in case of multiple probes for the same Agilent ID, log-intensities were averaged. Control probes were remove prior to analysis.
|
| |
|
| Submission date |
Dec 21, 2010 |
| Last update date |
Jan 05, 2016 |
| Contact name |
Rekin's Janky |
| E-mail(s) |
[email protected]
|
| Organization name |
VIB
|
| Department |
Nucleomics Core
|
| Street address |
Herestraat 49 Box 816
|
| City |
Leuven |
| ZIP/Postal code |
B-3000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL11346 |
| Series (1) |
| GSE26228 |
C. elegans pdf-1 gene knockout effect |
|
