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Sample GSM743747 Query DataSets for GSM743747
Status Public on Jun 11, 2014
Title Male diet C liver tissue, biological rep2
Sample type RNA
 
Source name liver, diet C
Organism Felis catus
Characteristics gender: male
age: 9 months
tissue: liver
treatment: trans-fat, HFCS, and MSG diet
Treatment protocol Male offspring used in the following experiments were weaned onto the same diets as the dams and were maintained on their respective dietary regimens until they reached 9 months of age. The four dietary regimens used in this study were: [1] Standard Chow Control feline diet (Test Diet Purina catalog #5003); [2] MSG diet consisting of Control diet with 1.125% added Monosodium Glutamate (Diet A: Test Diet Purina catalog #5C1J); [3] Trans-fat/HFCS diet, containing 8.6% Trans fat and 24% HFCS (Diet B: Test Diet Purina catalog #5B4K); and [4] Trans-fat/HFCS and MSG diet, containing 8.6% Trans fat, 24% HFCS and 1.125% MSG (Diet C: Test Diet Purina catalog #5C1H).
Growth protocol Our study animals were bred from female Felis catus previously placed on one of 4 different dietary regimens for a period of 3 weeks prior to mating. The four dietary regimens used in this study were: [1] Standard Chow Control feline diet (Test Diet Purina catalog #5003); [2] MSG diet consisting of Control diet with 1.125% added Monosodium Glutamate (Diet A: Test Diet Purina catalog #5C1J); [3] Trans-fat/HFCS diet, containing 8.6% Trans fat and 24% HFCS (Diet B: Test Diet Purina catalog #5B4K); and [4] Trans-fat/HFCS and MSG diet, containing 8.6% Trans fat, 24% HFCS and 1.125% MSG (Diet C: Test Diet Purina catalog #5C1H). Following mating, the 4 groups of dams were maintained on their respective diets throughout the gestation and nursing period.
Extracted molecule total RNA
Extraction protocol Hepatic tissues (4-5 per diet group) were used for RNA extraction. Total RNA was prepared from snap-frozen liver tissue using the QIAGEN RNeasy® Kit according to the manufacturer's instructions. The integrity of the RNA was measured using a 2100 Bioanalyzer instrument and an RNA 6000 Nano LabChip assay (Agilent Technologies).
Label biotin
Label protocol Biotinylated ssDNA were prepared according to the standard Affymetrix protocol from 250ng total RNA (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Technical Manual, 2009, Affymetrix).
 
Hybridization protocol Following fragmentation, 5.5 ug of ssDNA was hybridized for 17 hr at 45°C on GeneChip(R) Human Gene 1.0 ST arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using the Affymetrix 3000 7G Scanner, and GeneChip Operating Software version 1.4 was used to produce .CEL files.
Description CAT# 8_(HuGene-1_0-st-v1)
Gene expression data from 9-month-old male diet C liver.
Data processing Microarray analysis was performed using the Partek genomic suite software version 6.4 (Partek, MO, USA). We imported the interrogating probes using the file HuGene-1_0-st-v1.na31.hg19.probeset.csv.zip downloaded from: http://www.affymetrix.com/estore/browse/products.jsp?productId=131453&categoryId=35676&productName=GeneChip-Human-Gene-1.0-ST-Array#1_3
Probe set data were summarized, background adjusted, and quantile normalized using the GC-Robust Multi-Array (GCRMA) algorithm, no log. A pre-background adjustment for probe sequence was also applied.
 
Submission date Jun 16, 2011
Last update date Jun 11, 2014
Contact name Marya Zia Zaidi
E-mail(s) mzia@kfshrc.edu.sa
Organization name KFSH&RC
Department Biological & Medical Research
Lab Cell Biology & Diabetes Research Unit
Street address 1 Takhassussi Road
City Riyadh
State/province Riyadh
ZIP/Postal code 11211
Country Saudi Arabia
 
Platform ID GPL10739
Series (1)
GSE30040 Expression data from feline liver tissue

Data table header descriptions
ID_REF
VALUE GC-RMA signal intensity

Data table
ID_REF VALUE
8095631 22966.4
8100860 17757.2
8048061 14964.1
8082805 13992
7917646 13026.2
8048052 11913.5
8138533 11657.5
7962570 11572.5
8138538 11187.2
8048038 10690.3
7960997 10593.6
8002562 10517.5
7962569 10317.5
7960960 10135.5
8123269 10031
8088044 9884.87
8123268 9848.53
8158955 9411.38
8095633 8972.43
7993424 8889.59

Total number of rows: 257101

Table truncated, full table size 3989 Kbytes.




Supplementary file Size Download File type/resource
GSM743747.CEL.gz 3.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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