|
| Status |
Public on Oct 03, 2008 |
| Title |
Circadian time 39 Liver_CT39 |
| Sample type |
RNA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
adult, male C57Bl/6J
|
| Growth protocol |
Mice were house in light-tight chambers and entrained to a 12 hours light, 12 hours dark environment before being released into constant darkness.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mice were euthanized in the dark and liver samples were quickly excised.
|
| Label |
biotin
|
| Label protocol |
Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated CTP and UTP.
|
| |
|
| Hybridization protocol |
The cRNA products were fragmented to 200 nucleotides or less, heated at 99 degrees C for 5 min and hybridized for 16 h at 45 degrees C. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.
|
| Scan protocol |
A confocal scanner was used to collect fluorescence signal at 3um resolution after excitation at 570 nm. The average signal from two sequential scans was calculated for each microarray feature.
|
| Description |
n/a
|
| Data processing |
Affymetrix Microarray Suite 5.0 was used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters. Border pixels were removed, and the average intensity of pixels within the 75th percentile was computed for each probe. The average of the lowest 2% of probe intensities occurring in each of 16 microarray sectors was set as background and subtracted from all features in that sector. Probe pairs were scored positive or negative for detection of the targeted sequence by comparing signals from the perfect match and mismatch probe features.
|
| |
|
| Submission date |
Jun 27, 2008 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Michael Hughes |
| E-mail(s) |
michael.evan.hughes@gmail.com
|
| Organization name |
UPenn
|
| Street address |
421 Curie Bvd, Brb 835
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE11923 |
High-temporal resolution profiling of mouse liver |
|
| Relations |
| Reanalyzed by |
GSE28622 |
| Reanalyzed by |
GSE119085 |
