|
| Status |
Public on Jun 01, 2011 |
| Title |
Ctrl-coc-P6-Technical-rep2-b |
| Sample type |
RNA |
| |
|
| Source name |
Rb1 control cochleas at P6, Pooled, Technical rep2
|
| Organism |
Mus musculus |
| Characteristics |
tissue: dissected cochlea
genotype/variation: wild type
age: P6
|
| Treatment protocol |
P6 or 2-month control and Rb1 cKO littermates were euthanized and the inner ear tissues were dissected in DMEM-F12 medium. Dissected tissues were collected in RNAlater solution for RNA extraction.
|
| Growth protocol |
Mice were maintained in MGH animal facility.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with Qiagen Rneasy Mini Kit according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the Affymetrix Small Sample Target Labeling Assay Version II protocol from 0.3-2 ug total RNA.
|
| |
|
| Hybridization protocol |
Following the Affymetrix gene chip standard protocol of hybridization Wash and stain. 15 ug of fragmented cRNA were hybridized on GeneChip MOE430 A or B Genome Array. The arrays were placed in Affymetrix Genechip Hybridization Oven 640, incubated for 16 hours at 45C, 60rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix Gene chip Scanner 3000 7G.
|
| Description |
Gene expression data from P6 Rb1 control cochleas
rb-ctrl-coc-2b
|
| Data processing |
The data were analyzed with dChip, normalized using Invariant set normalization method. The expression values of Model-based expression indexes (MBEI) were created with PM/MM difference model using the default settings. The data were also analyzed with MAS 5.0 to obtain Present/Absent calls.
|
| |
|
| Submission date |
Dec 01, 2010 |
| Last update date |
Jun 01, 2011 |
| Contact name |
Zheng-Yi Chen |
| E-mail(s) |
Zheng-Yi_Chen@meei.harvard.edu
|
| Phone |
617-573-3673
|
| Organization name |
MEEI
|
| Department |
Otolaryngology
|
| Lab |
Eaton Peabody Lab
|
| Street address |
243 Charles Street
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02114 |
| Country |
USA |
| |
|
| Platform ID |
GPL340 |
| Series (1) |
| GSE25732 |
Expression data from Pou4f3-Rb1 cKO and control inner ear |
|
