|
| Status |
Public on Sep 22, 2015 |
| Title |
aptf-1_4 in pretzel-stage embryos |
| Sample type |
RNA |
| |
|
| Source name |
aptf-1(gk794) mutant, replicate 4
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
tissue: whole animal
gender: hermaphrodite
age: pretzel-stage embryo
genotype/variation: aptf-1(gk794) mutant pretzel-stage embryos
|
| Treatment protocol |
For performing the experiment ‘‘Low RNA Input linear Amplification Kit Plus, One Color’’ protocol (Agilent Technologies, Inc. 2007; Cat. Nu: 5188–5339) and the Agilent RNA Spike-In Kit for One color (Agilent Technologies, Inc. 2007; Cat. Nu: 5188–5282)were used following the manufacturer’s standard protocol.
|
| Growth protocol |
C. elegans worms were grown on Nematode Growth Medium (NGM) plates seeded with E. coli OP50 at 21.5°C. For each sample approximately 3000 pretzel-stage embryos were picked individually with a platinum wire pick and were immediately placed into a tube containing one ml of Trizol (Invitrogene).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from the Trizol using standard procedure.
|
| Label |
Cy3
|
| Label protocol |
200 ng of total RNA were used as a starting material to prepare cDNA. cDNA synthesis and in vitro transcription (IVT) were performed according to the manufacturer’s recommendation. Quantity and efficiency of the labeled amplified cRNA were determined using the NanoDrop ND-1000 UV-VIS Spectrophotometer version 3.2.1.
|
| |
|
| Hybridization protocol |
The hybridizations were performed for 17 hours at 10 rpm and 65uC in the Hybridization Oven (Agilent).
|
| Scan protocol |
Cy3 intensities were detected by one-color scanning using an Agilent DNA microarray scanner (G2505B).
|
| Description |
Gene expression in aptf-1(gk794) mutant pretzel-stage embryos
|
| Data processing |
Intensity data were extracted using Agilent’s Feature Extraction (FE) software (version 9.5.3.1) including a quality control based on internal controls using Agilent’s protocol GE1_107_Sep09. All chips passed the quality control and were analyzed using the Limma package of Bioconductor.
|
| |
|
| Submission date |
Sep 21, 2015 |
| Last update date |
Oct 05, 2015 |
| Contact name |
Michal Turek |
| E-mail(s) |
[email protected]
|
| Organization name |
Max Planck Institute for Biophysical Chemistry
|
| Department |
Sleep and Waking
|
| Lab |
15800
|
| Street address |
Am Fassberg 11
|
| City |
Goettingen |
| ZIP/Postal code |
37077 |
| Country |
Germany |
| |
|
| Platform ID |
GPL11346 |
| Series (1) |
| GSE73283 |
Transcriptional profiling of C. elegans aptf-1(gk7954) mutant in pretzel-stage embryos. |
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