|
| Status |
Public on Nov 10, 2015 |
| Title |
E12.5 mutant_3 |
| Sample type |
RNA |
| |
|
| Source name |
whole cortex e12.5
|
| Organism |
Mus musculus |
| Characteristics |
strain: mixed background
genotype: Pbx1 mutant
developmental stage: E12.5
tissue: cortext
|
| Treatment protocol |
no additional treatment were performed
|
| Growth protocol |
cortex was dissected from mouse embryos at developmental stage E12.5
|
| Extracted molecule |
total RNA |
| Extraction protocol |
corteces were preserved in RNAlater awaiting genotyping; RNA was extracted using 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
|
| Data processing |
Raw signal intensities were extracted with Feature Extraction v10.5 software. We extract the raw signal intensities, log them and quantile normalize the results. 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 greater probability that a gene is DE than non-DE
|
| |
|
| Submission date |
Sep 21, 2015 |
| Last update date |
Nov 10, 2015 |
| Contact name |
olga golonzhka |
| Organization name |
UCSF
|
| Department |
psychiatry
|
| Street address |
1550 4th street
|
| City |
san francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
| |
|
| Platform ID |
GPL7202 |
| Series (2) |
| GSE73286 |
gene expression analysis in Pbx1; Emx1-cre mutant cortex at embryonic day 12.5 |
| GSE73288 |
gene expression analysis in Pbx1; Emx1-cre mutant cortex at embryonic day |
|
