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Sample GSM106162 Query DataSets for GSM106162
Status Public on Apr 28, 2006
Title High weight gainer KOZAK2_ABI_HYP_H4
Sample type RNA
 
Source name Hypothalamus
Organism Mus musculus
Characteristics Mouse hypothalamus
Extracted molecule total RNA
Extraction protocol Tissues were quickly removed and frozen in liquid nitrogen and stored at -80C for subsequent preparation of total RNA. Total RNA was isolated using TRI-Reagent (Molecular Research Center Inc. Cincinnati, Ohio) with modifications to remove DNA using the Qiagen RNAeasy columns and DNaseI Kit (Qiagen, Valencia, CA). RNA was stored at –70C in RNase-free H2O supplemented with the RNase inhibitor Superasin (Ambion, Austin, TX) as per manufacturers directions. Quality and quantity of RNA was determined using a Agilent Bioanalyzer as per manufacturers procedures (Agilent Technologies, Palo Alto, CA).
Label DIG-UTP
Label protocol 1 ug of total RNA was used to transcribe DIG-labeled cRNA using Applied Biosystems Chemiluminescent RT-IVT Kit V2.0.
 
Hybridization protocol Microarray hybridization (using twenty micrograms of fragmented, DIG-labeled cRNA) and processing were performed according to Applied Biosystems protocols.
Scan protocol Chemiluminescence detection, imaging, auto gridding, and image analysis was done according to Applied Biosystems protocols and the 1700 Chemiluminescent Microarray Analyzer Software v. 1.0.3.
Description Pooled hypothalamus RNA samples from 20 C57BL/6J mice with 'high' weight gain after 6 weeks on a high fat diet (D12331;Research Diets, New Brunswick, NJ), followed by 2 weeks of low fat diet, and 6 weeks on a high fat diet. Microarrays were performed in quadruplicate, H1, H2, H3, H4.
Data processing Signal intensities across microarrays were normalized using the trimmed means scale (Spotfire DecisionSite for Functional Genomics, Somerville, MA).
 
Submission date Apr 21, 2006
Last update date Sep 25, 2006
Contact name Jessica C Hogan
E-mail(s) hoganjc@pbrc.edu
Phone 225-763-3143
Fax 225-763-0273
Organization name Pennington Biomedical Research Center
Department Molecular Genetics
Street address 6400 Perkins Rd.
City Baton Rouge
State/province LA
ZIP/Postal code 70808
Country USA
 
Platform ID GPL2995
Series (1)
GSE4697 Effect of a high fat diet on the hypothalami of mice susceptible to diet-induced obesity KOZAK2_ABI_HYP

Data table header descriptions
ID_REF
VALUE same as UNF_VALUE but with flagged values removed
SIGNAL_RAW Raw signal intensity
STDEV Noise/background signal intensity
S2N Signal to noise ratio is equal to SIGNAL_RAW/STDEV
CV Coefficient of variation of signal intensity based on the error model built in the Applied Biosystems image analysis software
FLAG Quality of each probe
DETECTION_FLAG Detectable: 1 (S2N>3 and FLAG<5000); not detectable 0 (S2N<3 or FLAG>5000)
UNF_VALUE Signal normalized using the trimmed means scale (Spotfire DecisionSite for Functional Genomics, Somerville, MA)

Data table
ID_REF VALUE SIGNAL_RAW STDEV S2N CV FLAG DETECTION_FLAG UNF_VALUE
297784 4.216900288 20018.97 355.58 56.3 0.1 0 1 4.216900288
297907 174.83 122.63 1.43 0.71 0 0 0.036827103
297912 0.544271432 2583.83 203.03 12.73 0.13 0 1 0.544271432
297935 0.257425307 1222.08 311.01 3.93 0.27 0 1 0.257425307
297990 0.139080611 660.26 148.76 4.44 0.25 0 1 0.139080611
297993 155.03 155.03 -1.13 0.89 1 0 0.032656328
298000 3.606315635 17120.33 324.56 52.75 0.13 0 1 3.606315635
298038 1.082006543 5136.63 217.47 23.62 0.14 0 1 1.082006543
298121 0.087605239 415.89 76.38 5.44 0.23 0 1 0.087605239
298130 646.15 646.15 0.73 1.38 1 0 0.136108407
298143 2.596313947 12325.53 266.41 46.26 0.1 0 1 2.596313947
298150 317.25 122.02 2.6 0.41 0 0 0.066827195
298151 0.264066951 1253.61 238.42 5.26 0.22 0 1 0.264066951
298155 194.62 163.2 1.19 0.85 0 0 0.040995772
298165 3.786758541 17976.95 346.31 51.91 0.13 0 1 3.786758541
298174 0.366267798 1738.79 211.55 8.22 0.18 0 1 0.366267798
298188 0.283701192 1346.82 92.57 14.55 0.15 0 1 0.283701192
298200 40.9947548 194615.17 2478.51 78.52 0.1 0 1 40.9947548
298246 206.08 206.08 -0.71 1.41 1 0 0.043409766
298248 228.82 186.4 1.23 0.83 0 0 0.048199839

Total number of rows: 33012

Table truncated, full table size 1742 Kbytes.




Supplementary data files not provided

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