|
| Status |
Public on Jul 01, 2014 |
| Title |
WT_50.9 |
| Sample type |
RNA |
| |
|
| Source name |
E9.5 female mouse embryo, WT
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: mixed C3HeB/FeJ
genotype: Chd7+/+
gender: female
age: E9.5
tissue: embryo
|
| Treatment protocol |
Matings between heterozygous Whirligig males and females were set up. Female Whirligig mice (Chd7Whi/+) were checked daily for the presence of a copulation plug. The day on which the vaginal plug was observed was counted as E0.5. Pregnant female Whirligig mice (Chd7Whi/+) were sacrificed by cervical dislocation, the uterus was removed and the embryos were dissected from the yolk-sacs.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA isolation was performed from four biological replicates from E9.5 wildtype, Chd7Whi/+ and Chd7Whi/Whi female mouse embryos using the Trizol (Invitrogen) method according to the manufacturer's recommendations. Afterwards, the samples were DNase I (Sigma) treated in order to remove DNA contamination. RNA quality was determined using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) microfluidic electrophoresis. Only samples with comparable RNA integrity numbers were selected for microarray analysis.
|
| Label |
Cy3
|
| Label protocol |
Microarrays were done using the "Low RNA Input linear Amplification Kit Plus, One Color" protocol (Agilent Technologies, Inc. 2007; Cat. Nr: 5188-5339) and the Agilent RNA Spike-In Kit for One color (Agilent Technologies, Inc. 2007; Cat. N°: 5188-5282) following the manufacturer's standard protocol.
|
| |
|
| Hybridization protocol |
The hybridizations were performed for 17 hours at 10 rpm and 65°C in the Hybridization Oven (Agilent). Washing and staining of the arrays were done according to the manufacturer's recommendation.
|
| Scan protocol |
Cy3 intensities were detected by one-color scanning using an Agilent DNA microarray scanner (G2505B) at 5 micron resolution. Scanned image files were visually inspected for artifacts and then analyzed.
|
| Description |
WT
whirligig mouse line (Bosman et al. 2005).
|
| Data processing |
Agilent's Feature Extraction Software Version 10.7.3.1 using default parameters. Data were quantile normalized using R and Bioconductor package limma.
|
| |
|
| Submission date |
May 02, 2013 |
| Last update date |
Jul 01, 2014 |
| Contact name |
Gabriela Salinas |
| E-mail(s) |
Gabriela.Salinas-Riester@medizin.uni-goettingen.de
|
| Organization name |
Universitaetsmedizin Goettingen
|
| Department |
Department of Pathology
|
| Lab |
NGS Integrative Genomics
|
| Street address |
Kreuzbergring 57
|
| City |
Goettingen |
| State/province |
Lower-Saxony |
| ZIP/Postal code |
37075 |
| Country |
Germany |
| |
|
| Platform ID |
GPL10333 |
| Series (1) |
| GSE46591 |
CHD7 regulates gene networks involved in neural crest cell migration and axon guidance |
|
