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Sample GSM1132992 Query DataSets for GSM1132992
Status Public on Jul 01, 2014
Title KO.htz_50.2
Sample type RNA
 
Source name E9.5 female mouse embryo, Chd7 heterozygote
Organism Mus musculus
Characteristics strain/background: mixed C3HeB/FeJ
genotype: Chd7Whi/+
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 heterozygote CHD7_KO
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

Data table header descriptions
ID_REF
VALUE Processed Cy3 signal intensity (Agilent gProcessedSignal) = Normalized signal intensity

Data table
ID_REF VALUE
1 2.418412e+004
2 3.119512e+000
3 3.104459e+000
4 3.088446e+000
5 3.072541e+000
6 3.056009e+000
7 3.038809e+000
8 3.022022e+000
9 3.004802e+000
10 2.987565e+000
11 2.970088e+000
12 3.752936e+002
13 1.202269e+001
14 2.779230e+003
15 1.803636e+002
16 4.470328e+003
17 3.946522e+003
18 2.854592e+000
19 2.839231e+000
20 2.829487e+001

Total number of rows: 44397

Table truncated, full table size 856 Kbytes.




Supplementary file Size Download File type/resource
GSM1132992_US22502691_252665512997_S01_GE1_107_Sep09_1_4.txt.gz 2.1 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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