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Sample GSM2560 Query DataSets for GSM2560
Status Public on Nov 11, 2002
Title 22-oct-2002-BrainDsubA-ab150
Sample type RNA
 
Source name brain/hippocampus
Organism Mus musculus
Extracted molecule total RNA
 
Description Dietary effects of arachidonate-rich fungal oil and fish oil on murine hepatic and hippocampal gene expression, Lipids in Health and Disease 2002.
Diet contained 90% fat-free AIN93G rodent diet in powder form (Lot 9350-5, Dyets, Inc., Bethlehem, PA), 0.4% milk fat, 1.2% palm olein, 1.9% Trisun sunflower oil, 1.5% soybean oil and 2.1-5.1% medium chain triacylglycerol oil (all of the above ingredients except the AIN93G were from Nestlé affiliated companies). Part of the medium chain triacylglycerol oil in control diet was replaced with: 1.1% fungal oil (providing 0.5 dietary wt% AA and 1.0en%). Food was maintained at -80°C in daily aliquots under liquid N2, thawed each afternoon before administration to mice, and uneaten food was discarded daily.
Prior to actual experimentation, test dissections were made on identical mice to perfect the dissection techniques at Porsolt & Partners Pharmacology (Paris, France).
Male Rj:NMRI mice from Elevage Janvier, Le Genest-Saint-Isle France, weighing 10-11 g at delivery and 33-51 grams on experimental d 42, were housed 10 per cage in wire cages with bedding and normal light cycle. Mice received ad libitum quantities of distilled water and purified powdered diets (7.5 g/mouse) in ceramic cups (10/group) from d 1-57 or 58, and were thereafter sacrificed in the morning by cervical dislocation over these last 2 experimental days. Food was not removed the night before, and since nocturnal mice are known to eat during the normal period dark cycle employed, the mice could have been fasted 0-6 h at sacrifice. Mice were thus not completely fasted at sacrifice, a complete fast being 12-16 h. After feeding diets to 10 mice per group, 5 mice were randomly selected for inclusion in hippocampal gene expression analysis. From these same 5 mice, the hippocampus was dissected from the mice according to standard protocols (Porsolt & Partners Pharmacology, Boulogne-Billancourt, France), rinsed as described for livers, cut into 17-50 mg subsections, and frozen as described for livers. Hippocampal lipid analysis was performed according to standard methods at Lipomics, Inc. (U.S.A) on individual mice (n=5).
Hippocampal tissue was extracted from 5 individual mice per group and extracted separately using Qiagen RNeasy mini-kits (Basel, Switzerland) according to manufacturer instructions, except that RNeasy columns were impregnated with DNase I (Roche, Basel, Switzerland) to remove any genomic DNA contamination. A pool of 10 mg total hippocampal RNA was created from the 5 individual extractions prior to GeneChip analysis. All RNA samples (individual and pooled) were quantified with the RiboGreen RNA Quantification Kit (Molecular Probes, Eugene Oregon), then analyzed via agarose gel electrophoresis for intact 18S and 28S rRNA. All study samples were judged to contain sufficient amounts of high-quality RNA for hybridization to GeneChips. As another quality control measure, prior to hybridization with Affymetrix GeneChips (Affymetrix, Inc., Santa Clara, CA), we confirmed that pooled samples gave strong signals using Affymetrix test chips.
 
Submission date Oct 28, 2002
Last update date Mar 10, 2006
Contact name David Vilanova
E-mail(s) david.vilanova@rdls.nestle.com
Phone +41217858723
Organization name Nestle Research Center
Street address
City Lausanne
ZIP/Postal code 1012
Country Switzerland
 
Platform ID GPL75
Series (1)
GSE91 Effect of dietary oils on hippocampus and liver gene expression

Data table header descriptions
ID_REF
Positive Number of positive probe pairs
Negative Number of negative probe pairs
Pairs Number of probe set specific probe pairs on the array
Pairs_Used Pairs used
Pos_fraction Positive fraction
Pairs_InAvg Pairs in average
Log_Avg Log average
PM_Excess Number of probe pairs where PM/MM exceeds the ratio limit (10 by default)
MM_Excess Number of probe pairs where MM/PM exceeds 1/ratio limit (10 by default)
Pos/Neg Positive/Negative
VALUE Average Difference Intensity
ABS_CALL Whether a probe set is present, marginal, or absent

Data table
ID_REF Positive Negative Pairs Pairs_Used Pos_fraction Pairs_InAvg Log_Avg PM_Excess MM_Excess Pos/Neg VALUE ABS_CALL
aa000148_s_at 12 3 20 20 0.6 17 1.87 0 0 4 132 P
AA000151_at 6 4 20 20 0.3 18 -0.01 0 0 1.5 16 A
aa000380_s_at 12 0 20 20 0.6 19 3.31 1 0 Undef 238 P
aa000467_s_at 18 0 20 20 0.9 20 5.06 2 0 Undef 888 P
aa000469_at 16 1 20 20 0.8 17 4.88 0 0 16 621 P
aa000469_g_at 14 1 20 20 0.7 19 2.48 0 0 14 559 P
aa000750_s_at 17 2 20 20 0.85 19 3.03 0 0 8.5 519 P
aa002653_s_at 11 1 20 20 0.55 18 2.53 0 0 11 120 P
aa002704_at 8 2 20 20 0.4 17 0.91 0 0 4 21 P
aa002761_s_at 11 2 20 20 0.55 18 1.56 0 0 5.5 33 P
aa002925_s_at 9 1 20 20 0.45 18 1.59 0 0 9 -17 P
aa003078_s_at 12 1 20 20 0.6 18 2.48 0 0 12 53 P
aa003157_at 12 3 20 20 0.6 18 2.62 0 0 4 94 P
aa003161_s_at 5 5 20 20 0.25 19 -0.47 0 0 1 -32 A
aa003244_s_at 3 7 20 20 0.15 17 -0.4 0 0 0.4 -12 A
aa003358_s_at 16 1 20 20 0.8 19 4.41 0 0 16 321 P
aa004011_s_at 15 0 20 20 0.75 20 4.15 1 0 Undef 143 P
AA004127_at 5 5 20 20 0.25 18 0.4 0 0 1 55 A
aa008269_s_at 5 6 20 20 0.25 18 -0.74 0 0 0.8 7 A
aa008321_s_at 18 0 20 20 0.9 20 4.8 2 0 Undef 301 P

Total number of rows: 6584

Table truncated, full table size 317 Kbytes.




Supplementary data files not provided

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