|
| Status |
Public on Jun 03, 2015 |
| Title |
Basal Ganglia_E12.5_Control_Rep1 |
| Sample type |
RNA |
| |
|
| Source name |
control, ganglionic eminences and septum
|
| Organism |
Mus musculus |
| Characteristics |
strain: CD-1
genotype: Control
litter: 3.1
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 |
Control
Control_litter3.1
|
| 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 |
|
