|
Status |
Public on Jun 03, 2015 |
Title |
Basal Ganglia_E12.5_Otx2cKO_Rep2 |
Sample type |
RNA |
|
|
Source name |
Otx2cKO, ganglionic eminences and septum
|
Organism |
Mus musculus |
Characteristics |
strain: CD-1 genotype: Otx2 cKO litter: 1.3 gender: Female developmental stage: E12.5 tissue: ganglionic eminences and septum
|
Growth protocol |
Subpallial (ganglionic eminences and septum) tissue wasmicrodissected from E12.5 female brains (n=4 control, n=3 CKO), snap frozen, and stored at -80oC
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was isolated using the Qiagen RNAeasy kit.
|
Label |
Cy3
|
Label protocol |
RNA was amplified (labeled with Cy3-CTP)withAgilent low RNA input fluorescent linear amplification kits, and cRNA was assessed using the Nandrop ND-100 (Nanodrop Technologies, Inc., Wilmington DE). Equal amounts of Cy3 labeled target were hybridized to Agilent whole mouse genome 4x44K Ink-jet arrays, by theUCSF Genomics Core.
|
|
|
Hybridization protocol |
Hybridization were performed for 14 hrs, according to the Agilent protocol.
|
Scan protocol |
Arrays were scanned using the Agilent microarray scanner.
|
Description |
RxCre cKO KO_litter1.3
|
Data processing |
Raw signal intensities were extracted with Agilent Feature Extraction v10.5 software. Significant changes in gene expression were defined as B value greater than zero. B = log 10 posterior odds ratio, ratio between the probability that a given gene is differentially expressed (DE)over the probability that a given gene is not differentially expressed.B≥0 means equal or greaterprobability that a gene is DE than non-DE
|
|
|
Submission date |
Jun 03, 2015 |
Last update date |
Jun 08, 2015 |
Contact name |
John Rubenstein |
E-mail(s) |
John.Rubenstein@ucsf.edu
|
Organization name |
UCSF
|
Department |
Psychiatry
|
Lab |
Rubenstein Lab
|
Street address |
1550 4th Street
|
City |
San Francisco |
State/province |
CA |
ZIP/Postal code |
94158 |
Country |
USA |
|
|
Platform ID |
GPL7202 |
Series (2) |
GSE69547 |
Otx2 controls regional patterning within the MGE and regional identity of the septum [Agilent] |
GSE69727 |
Otx2 controls regional patterning within the MGE and regional identity of the septum |
|