|
| Status |
Public on Jun 11, 2014 |
| Title |
Male control diet liver tissue, biological rep2 |
| Sample type |
RNA |
| |
|
| Source name |
liver, control diet
|
| Organism |
Felis catus |
| Characteristics |
gender: male
age: 9 months
tissue: liver
treatment: control 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# 2_(HuGene-1_0-st-v1)
Gene expression data from 9-month-old male control diet 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 |
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