|
| Status |
Public on Jul 12, 2012 |
| Title |
Hes_3minus |
| Sample type |
RNA |
| |
|
| Source name |
Hes5::GFP-
|
| Organism |
Mus musculus |
| Characteristics |
strain: J1
cell type: mESC
genotype/variation: Hes5::GFP-
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Illumina protocol from total RNA.
|
| |
|
| Hybridization protocol |
Following fragmentation, cRNA were hybridized for Illumina GX mouse WG-6 Array. Slides were washed and stained in the Illumina instrument.
|
| Scan protocol |
Slides were scanned using Illumina iScanner
|
| Description |
Hes_3minus
|
| Data processing |
The data were analyzed with GenomeStudio using Illumina default analysis settings. No normalization and background correction are performed.
1. Illumina data are loaded into GenomeStudio and produced the raw data automatically. There is no normalization and background correction applied during this process. The data will be automatically normalized in Partek. To avoid shifting the data, Partek doesn't recommend to use background correction. Otherwise the negative intensities in the data will create problems for the following analysis.
2. Data from GenomeStudio is exported in a custom Partek report file for seamless importation into Partek. Gene level option is chosen and the probe intensities are summarized and averaged for the same genes. The intensity is log2 transformed at the same time.
3. After the Partek version data is imported into Partek, there are options for normalization to be chosen. But it is not necessary to use normalization according to Partek. So there is no further background correction and normalization. The user assigned the factor (sample attributes) before ANOVA analysis and did one factor analysis.
|
| |
|
| Submission date |
Apr 19, 2012 |
| Last update date |
Jul 12, 2012 |
| Contact name |
Jeffrey Zhao |
| Organization name |
Memorial Sloan Kettering Cancer Center
|
| Department |
Genomics Core
|
| Street address |
1275 York Avenue
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL13824 |
| Series (1) |
| GSE37446 |
Sequential stage specific reporter line analysis (SSRLA) of 3 BAC transgenic mESC lines |
|
