|
| Status |
Public on Jul 01, 2009 |
| Title |
Optic nerves from P14 wild type |
| Sample type |
RNA |
| |
|
| Source name |
Optic nerves dissected from P14 wild type
|
| Organism |
Mus musculus |
| Characteristics |
genotype: CD1 wild type
Sex: male
cell type: 8 optic nerves used
|
| Treatment protocol |
Optic nerves were not treated after dissection from postnatal mice
|
| Growth protocol |
Optic nerves from LIF knockout and wild type mice. Postnatal day 10- 10 optic nerves, postnatal day 14- 8 optic nerves, postnatal day 35 (adult)- 4 optic nerves
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using TRIzol extraction method
|
| Label |
biotin
|
| Label protocol |
500 ng total RNA labelled using the Illumina TotalPrep RNA amplification kit. Single stranded RNA (cRNA) was generated and labeled by incorporating biotin-16-UTP.
|
| |
|
| Hybridization protocol |
750 ng of biotin-labeled cRNA was hybridized for 16 hours to Illumina Sentrix mouseref-8 expression beadchips
|
| Scan protocol |
Hybridized biotinylated cRNA was detected with streptavidin-Cy3 and quantitated using Illuminas beadstation 500GX genetic analysis systems scanner
|
| Description |
Investigation of leukemia inhibitory factor effect on oligodendrocyte development and myelination in the postnatal optic nerve
|
| Data processing |
Preliminary analysis of the scanned data was performed using Illumina BeadStudio software. The primary Illumina data is returned from the scanner in the form of an “.idat” file which contains single intensity data values/gene following the computation of a trimmed mean average for each probe type represented by a variable number of bead probes/gene on the array. The Bead Studio software returns information on the number and standard deviation of all the bead measurements per probe/gene as well as a detection threshold based on a comparison between the measured intensity calculated for a single probe/gene and the intensities measured for a large number of negative control beads built-in to the BeadChip arrays (D = % above negative/100, 1 = perfect, i.e. the intensity value of a gene is greater than all the intensities for every negative control tested). Any gene consistently below D=.99 for all samples was eliminated from further analysis. This background filter resulted in the removal of approximately 20% of all the genes on the Illumina array (4,938 background genes out of a total of 24,527 RefSeq genes). Further filtering removed 1,688 genes without a meaningful HUGO gene name. Overall differences in gene expression between samples were calculated by a global normalization method based on total intensity counts for each array. A normalization factor was determined by dividing the average total intensity by the true total intensity. Each intensity value was multiplied by its appropriate normalization factor.
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| |
|
| Submission date |
Jul 01, 2008 |
| Last update date |
Apr 10, 2014 |
| Contact name |
Philip Lee |
| Organization name |
NIH/NICHD
|
| Street address |
35 Lincoln Drive
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL6103 |
| Series (1) |
| GSE11935 |
Leukemia inhibitory factor regulates timing of oligodendrocyte development and myelination in postnatal optic nerve |
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