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Sample GSM579279 Query DataSets for GSM579279
Status Public on Aug 17, 2010
Title T00320753
Sample type RNA
 
Source name 076
Organism Mus musculus
Characteristics strain: C57BL/6J
age: 56-80 days
tissue region: ORB
region name: Orbital Cortex
condition: SD
specimen: 311-0131
time of day: ZT6
Extracted molecule total RNA
Extraction protocol Laser microdissection using the Leica LMD6000 was carried out on tissue sections (10 um) lightly stained with cresyl violet. Tissue was isolated into RLT buffer (Qiagen) and purified using the RNeasy kit (Qiagen). Using 5 ng total RNA as starting material, a two-round RNA amplification (Ambion MessageAmp II kit) was used to produce sufficient cDNA for biotin-labeling and hybridization to microarrays.
Label biotin
Label protocol Following the second round of reverse transcription, second-strand cDNA synthesis, and purification of double-stranded cDNA, in vitro transcription was performed using T7 RNA polymerase in the presence of Biotin-11-UTP. Purified cRNA (10 µg) was fragmented to uniform size (~0.1 kb).
 
Hybridization protocol Samples were applied to CodeLink Mouse Whole Genome Bioarrays (formerly supplied by GE Healthcare, Piscataway, NJ; now supplied by Applied Microarrays, Inc, Tempe, AZ) in hybridization buffer. Arrays were hybridized (37°C for 18 h) in a shaking incubator, washed in 0.75X Tris-buffered saline (pH 7.6) at 46°C for 1 h, and stained with Cy5-Streptavidin dye conjugate for 30 min.
Scan protocol Rinsed and dried arrays were scanned with a GenePixTM 4000B scanner [Molecular Devices, (formerly Axon Instruments), Sunnyvale, CA] at 5 µm resolution.
Description sample barcode: T00320753
Data processing Codelink Expression Analysis software (Applied Microarrays, Inc, Tempe, AZ) was used for gridding and feature intensity extraction from the scanned array images. quantile normalization followed by COMBAT
 
Submission date Aug 13, 2010
Last update date Aug 16, 2010
Contact name Changkyu Lee
E-mail(s) changkyul@alleninstitute.org
Phone (206)548-7085
Organization name Allen Institute for Brain Science
Street address 551 N 34th St
City Seattle
State/province WA
ZIP/Postal code 98103
Country USA
 
Platform ID GPL2897
Series (1)
GSE23628 Sleep Deprivation and Recovery Sleep for 7 Regions of Mouse Brain.

Data table header descriptions
ID_REF
VALUE quantile normalized signal intensity

Data table
ID_REF VALUE
96020 3.1478
96021 4.0622
96022 73.403
96023 1468.3
96024 137.46
96025 27.001
96027 2729.5
96028 1.789
96029 13.753
96030 481.43
96031 5.8574
96032 46.297
96034 50.016
96035 2.4393
96036 419.92
96037 25.287
96038 112.55
96039 372.17
96040 5.1494
96043 68.241

Total number of rows: 35061

Table truncated, full table size 466 Kbytes.




Supplementary file Size Download File type/resource
GSM579279.txt.gz 1.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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