NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM301372 Query DataSets for GSM301372
Status Public on Oct 03, 2008
Title Circadian time 42 Liver_CT42
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

Data table header descriptions
ID_REF
VALUE signal calculated by gcRMA implemented in 'R'

Data table
ID_REF VALUE
1415670_at 12872.9
1415671_at 18740.6
1415672_at 26228.8
1415673_at 3644.6
1415674_a_at 4972
1415675_at 2305.7
1415676_a_at 29693.3
1415677_at 30148.2
1415678_at 11024.7
1415679_at 27006.8
1415680_at 3093.3
1415681_at 8221.4
1415682_at 3266
1415683_at 16573
1415684_at 10135.5
1415685_at 8243.2
1415686_at 10220.1
1415687_a_at 46304.6
1415688_at 15003.5
1415689_s_at 3081.8

Total number of rows: 45101

Table truncated, full table size 750 Kbytes.




Supplementary file Size Download File type/resource
GSM301372.CEL.gz 3.7 Mb (ftp)(http) CEL
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap