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Sample GSM823875 Query DataSets for GSM823875
Status Public on Jun 18, 2012
Title Liver_Female_CF_rep2
Sample type RNA
 
Source name Whole liver
Organism Mus musculus
Characteristics strain: C57BL/6
Sex: Female
age: 3-weeks old
genotype: CF
Growth protocol At 21 days of age, mice were weaned onto an enriched diet (9F Sterilizable Rodent Diet 7960, Harlan Teklad, Madison, WI) and were provided a Colyte solution (peg-3350 & electrolytes for oral solution – Schwarz Pharma, Milwaukee, WI) in place of water at half-strength since at full strength it causes adverse effects in non-CF mice. Mice were sacrificed at 23 days.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the RNeasy Midi kit (Qiagen Inc, Valencia, CA. DNase treatment was performed in the column prior to elution. Biotin labeled cRNA was prepared uisng Illumina TotalPrep RNA Amplification kit (Applied Biosystems/Ambion, Austin, TX).
Label Cy3
Label protocol Samples were labeled with Cy3 following Illumina's protocol
 
Hybridization protocol cRNA was hybridized to Beadchips following Illumina's instructions
Scan protocol Beadchips were scanned using Illumina BeadArray Reader
Description lipid synthesis, nutrition, adipose storage
Data processing Data was initially processed with Illumina GenomeStudio software to assess quality control. Raw data was transferred to Integromics Biomarker Discovery for TIBCO Spotfire software (IBD, Madrid, Spain) where data was normalized using Illumina normalization: forcePositive as background correction, log2 as variance stabilization method, and quantile as the normalization method. Wild type group was used as the reference group.
 
Submission date Oct 28, 2011
Last update date Jun 18, 2012
Contact name Aura Perez
E-mail(s) aura.perez@case.edu
Phone 216-368-6894
Organization name CWRU
Department Pediatrics
Street address 10900 Euclid Avenue
City Cleveland
State/province OH
ZIP/Postal code 44106-4948
Country USA
 
Platform ID GPL6885
Series (1)
GSE33319 Altered de novo lipogenesis contributes to low adipose stores in cystic fibrosis mice.

Data table header descriptions
ID_REF
VALUE Quantile normalized
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_2896528 11.00069213 0
ILMN_2721178 9.001136371 0
ILMN_3033922 10.28664231 0
ILMN_3092673 12.53595808 0
ILMN_2816356 6.210311218 0.4010025
ILMN_2808939 10.82566665 0
ILMN_2634564 8.575984361 0
ILMN_2737647 6.25828847 0.3120301
ILMN_2734484 9.658644258 0
ILMN_2952292 7.590693397 0
ILMN_2699078 6.147259073 0.5288221
ILMN_1213681 8.621774544 0
ILMN_2735413 9.809670639 0
ILMN_2735415 10.21323591 0
ILMN_2891688 9.948997637 0
ILMN_2637698 9.392366445 0
ILMN_2674228 8.652846733 0
ILMN_2601546 6.43562694 0.1052632
ILMN_1230831 5.990694146 0.8383459
ILMN_2848071 9.602044611 0

Total number of rows: 25697

Table truncated, full table size 810 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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