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Sample GSM303466 Query DataSets for GSM303466
Status Public on Mar 08, 2009
Title Gyk-1LWRC
Sample type RNA
 
Source name Strain: Gyk wildtype gender:female, age: 23 weeks, tissue: liver
Organism Mus musculus
Characteristics Liver, 6% fat diet, 12 weeks
Liver, 6% fat diet, 12 weeks
Treatment protocol Mice were fed a 6% fat chow diet from 11 weeks of age until sacrifice at 23 weeks of age.
Growth protocol These mice were fed a 4% fat chow diet until 11 weeks of age.
Extracted molecule total RNA
Extraction protocol Liver tissues were homogenized and total RNA extracted using Trizol reagent (Invitrogen, CA) according to the manufacturer’s instructions. RNA samples were isolated from liver tissues using a Qiagen RNeasy Kit and quality-checked with an Agilent 2100 Bioanalyzer (Foster City, CA).
Label biotin
Label protocol RNA samples queued for whole genome analysis using Illumina gene expression chips are first quanted using the ribogreen RNA quantitation kit. Samples are normalized to 11 ng per ul. 100 ng of normalized total RNA is used as a template for the synthesis of cDNA using Ambion cDNA synthesis kit AMIL1791. Newly synthesized cDNA becomes the template for the amplification and biotinylation of cRNA . Labeled cRNA is quanted (ribogreen) and normalized to 77 ng per ul.
 
Hybridization protocol 800 ng of labeled cRNA product is hybridized to prepared whole genome arrays and allowed to incubate overnight ( 16 –20 hrs) at 55 degrees C. Arrays are washed then stained with Cy3 labeled streptavadin. Excess stain is removed by washing and the arrays are dried and scanned on an Illumina BeadScan con-focal laser scanner.
Scan protocol Scanning was performed using Illumina BeadScan con-focal laser scanner.
Description None
Data processing Data were scaled and normalized using the rank invariant method in the Beadstudio software v. 1.5.1.3. (Illumina Inc.)
 
Submission date Jul 03, 2008
Last update date Mar 04, 2009
Contact name Josh Deignan
E-mail(s) jdeignan@mednet.ucla.edu
Organization name UCLA
Department Cardiology
Lab Aldons J. Lusis
Street address 675 Charles E Young Dr South, MRL 3220
City Los Angeles
State/province CA
ZIP/Postal code 90024
Country USA
 
Platform ID GPL4865
Series (2)
GSE11998 Gyk female heterozygous liver expression vs C57Bl/6J female wildtype control
GSE12000 Obesity study in transgenic and knockout animals

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
18S_rRNA_X00686_523-S 7354.2
GI_11079652-S 14.9
GI_21070949-S 26331.1
GI_21746160-S -54.2
GI_23346428-S 31.7
GI_23592945-S 21687.1
GI_23956057-S 13.2
GI_28476905-S 5943.3
GI_31981441-S -38.9
GI_31982339-S 32.3
GI_46909570-S 345.5
GI_6671508-S 10357.7
GI_6678306-S 21.1
GI_6679936-S 19896.8
GI_6753645-S 24.7
GI_7106304-S 52.3
IGHA_J00475$V00785_Ig_heavy_constant_alpha_135-S 141.8
IGHD_V00786_Ig_heavy_constant_delta_68-S 41.4
IGHG2C_J00479_Ig_heavy_constant_gamma_2C_715-S 30.5
IGHM_V00818_Ig_heavy_constant_mu_941-S 74.4

Total number of rows: 24048

Table truncated, full table size 556 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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