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Sample GSM860621 Query DataSets for GSM860621
Status Public on Mar 06, 2012
Title scr-control, biological rep2
Sample type RNA
 
Source name SV cells isolated from inguinal White adipose tissue
Organism Mus musculus
Characteristics strain: C57BL/6J
Sex: male
expression: sh-scr
agent: none
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from cells or tissues using Trizol (Invitrogen).
Label biotin
Label protocol cDNA was prepared using a T7 promoter-tailed oligo-dT primer, followed by second strand synthesis. Double-stranded cDNA was used as the template for in vitro transcription (IVT) catalyzed by T7 polymerase and containing biotinylated CTP and UTP. Biotinylated complementary RNA (cRNA) is purified using the RNeasy system (Qiagen).
 
Hybridization protocol The purified cRNA was fragmented for hybridization and purified by phenol/chloroform extraction and ethanol precipitation. The fragmented cRNA and several biotinylated control oligonucleotides (for quality control) were hybridized to a mouse 430_2 chip overnight at 45C.
Scan protocol Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.
Data processing Array normalization, expression value calculation and clustering analysis were performed using DNA-Chip Analyzer (dChip). The Invariant Set Normalization method was used to normalize arrays at probe cell level to make them comparable, and the model-based method was used for probe-selection and computing expression values.
 
Submission date Jan 11, 2012
Last update date Mar 06, 2012
Contact name Kosaku Shinoda
E-mail(s) [email protected]
Phone 415-476-9736
Fax 415-514-2346
URL http://www.diabetes.ucsf.edu/members/shingo-kajimura
Organization name University of California, San Francisco
Department UCSF Diabetes Center and Department of Cell and Tissue Biology
Street address 35 Medical Center Way
City San Francisco
ZIP/Postal code 94143-0669
Country USA
 
Platform ID GPL8321
Series (1)
GSE35011 PPARg agonists induce a white-to-brown fat conversion through stabilization of PRDM16 protein

Data table header descriptions
ID_REF
VALUE dChip signal intensity

Data table
ID_REF VALUE
AFFX-BioB-5_at 404.2
AFFX-BioB-M_at 687.1
AFFX-BioB-3_at 428.3
AFFX-BioC-5_at 1031.3
AFFX-BioC-3_at 1470.3
AFFX-BioDn-5_at 2938.3
AFFX-BioDn-3_at 5170.2
AFFX-CreX-5_at 13250.8
AFFX-CreX-3_at 14253.9
AFFX-DapX-5_at 259.5
AFFX-DapX-M_at 597
AFFX-DapX-3_at 720.4
AFFX-LysX-5_at 63
AFFX-LysX-M_at 78.8
AFFX-LysX-3_at 138.5
AFFX-PheX-5_at 59.1
AFFX-PheX-M_at 77.1
AFFX-PheX-3_at 104.7
AFFX-ThrX-5_at 53.5
AFFX-ThrX-M_at 84.8

Total number of rows: 22690

Table truncated, full table size 376 Kbytes.




Supplementary file Size Download File type/resource
GSM860621_BS2011012550.CEL.gz 2.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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