|
| Status |
Public on May 10, 2013 |
| Title |
wild-type control rep1 |
| Sample type |
RNA |
| |
|
| Source name |
wild-type control
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57Bl/6
genotype/variation: wild type
age: E16.5
tissue: whole embyronic eye
|
| Treatment protocol |
genetic knockout
|
| Growth protocol |
embryos
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was purified using an Ambion Rnaqueous kit following the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
500ng of RNA from each sample was amplified and biotin-labeled using an Ambion Illumina TotalPrep RNA Amplification kit.
|
| |
|
| Hybridization protocol |
Standard Illumina hybridization protocol
|
| Scan protocol |
Standard Illumina scan protocol
|
| Description |
C96.5
replicate 1
|
| Data processing |
The filtered (reduced) data set was generated, in which any transcript that was not detected in at least 5% of the samples was removed. Also, The quantile distribution is estimated from the project samples, and after normalizing each sample's quantile distribution to the overall quantile distribution, negative values in the quantile distribution of the individual sample were censored (assigned as 1) , or 'scrunched' to the range 1-2. The scrunch procedure is a simple transformation of the form: x_transformed = {(x-min(x)) / (2 – min(x)) + 1, x < 2}, x >= 2 where x is the signal value of any particular gene/probe ID for any particular specimen.
|
| |
|
| Submission date |
May 09, 2013 |
| Last update date |
May 10, 2013 |
| Contact name |
Whitney E Heavner |
| E-mail(s) |
whitney.heavner@nih.gov
|
| Organization name |
National Institutes of Health
|
| Department |
NINDS
|
| Lab |
Molecular Neurobiology Section
|
| Street address |
Building 35 Rm 2B-203
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL6887 |
| Series (1) |
| GSE46796 |
Genome-wide analysis of Sox2-ablated optic cups compared with wild-type control optic cups at E16.5 |
|
