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Sample GSM1697397 Query DataSets for GSM1697397
Status Public on Jun 15, 2016
Title 86241_23_DUODENUM_MGI_GENE-3
Sample type RNA
 
Source name ob control_DUODENUM
Organism Mus musculus
Characteristics group: ob control
genotype: ob lean control (Lepob, heterozygote from the colony)
tissue: DUODENUM
animal: 23
Growth protocol Nine-week-old male, ob/ob (B6.V-Lepob/J), and ob lean control (Lepob, heterozygote from the colony) mice were purchased from Jackson Lab (Bar Harbor, Main) and acclimatized to a constant temperature and humidity (72°F and 50% relative humidity with a 12 h light and dark cycle from 05:00 h to 17:00 h) and had free access to food (LabDiet 5K20, LabDiet, St. Louis, MO) and water. At the age of twelve weeks, all animals were fasted for four hours in the morning and euthanized at 1pm under isoflurane anathesia. Nine-week-old male, C57BL/6J mice were purchased from Jackson Lab (Bar Harbor, Main) and acclimatized to a constant temperature and humidity (72°F and 50% relative humidity with a 12 h light and dark cycle from 05:00 h to 17:00 h) for one week with free access to food (LabDiet 5001, LabDiet, St. Louis, MO) and water. After acclimation, half of the mice (n=6) were kept on the regular chow diet (LabDiet 5001) and half of them (n=6) were switched to TD93075 (Harlan Teklad, Madison, Wisconsin), a high-fat diet with 54.8%Kcal from fat for four weeks. At the end of the study, all animals were fasted for four hours in the morning and euthanized at 1pm under isoflurane anesthesia.
Extracted molecule total RNA
Extraction protocol Gastrointestinal tissues (whole stomach and about 1cm of intestinal samples from the middle of each part of the intestine) were collected. Finally a 1cm3 segment of the inferior right lobe of the liver was taken. Segments were immediately snap frozen in liquid nitrogen and stored at -80°C for subsequent RNA extraction. RNA extraction was performed using the RNeasy Mini kit (Qiagen Inc, Valencia, Calif). Total RNA yield and purity was estimated by UV spectroscopy (Nanodrop ND-1000 Spectrophotometer; Nanodrop Technologies, Wilmington, DE, USA) and RNA quality was assessed on an Agilent 2100 Bioanalyzer. Subsequently mRNA expression analysis was carried out.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug PolyA mRNA (Expression Analysis Technical Manual, 2001, Affymetrix).
 
Hybridization protocol The biotinylated cRNA was prepared and hybridized to the Mouse 430A_2.0 GeneChip in accordance with Affymetrix protocols.
Scan protocol GeneChips were scanned by the Affymetrix GeneChip Scanner.
Description 86241_23_DUODENUM_MGI_GENE-3
Data processing Microarray data was preprocessed using RMA implemented in R with BrainArray custom CDF.
 
Submission date May 27, 2015
Last update date Jun 15, 2016
Contact name Jing Chen
Organization name CCHMC
Street address 3333 Burnet Ave
City Cincinnati
State/province OH
ZIP/Postal code 45229
Country USA
 
Platform ID GPL19559
Series (1)
GSE69306 Significant obesity associated gene expression changes are in the stomach but not intestines in obese mice

Data table header descriptions
ID_REF
VALUE Log2 RMA signal

Data table
ID_REF VALUE
100008567_at 6.2762775
100009600_at 4.923826155
100012_at 3.694693072
100017_at 7.297460583
100019_at 7.888583104
100034251_at 7.479607088
100034739_at 4.158821674
100034748_at 4.156695405
100036520_at 3.963137125
100036521_at 8.492526725
100036523_at 4.281409659
100036768_at 5.018116081
100037258_at 8.817257261
100037262_at 4.356176601
100037278_at 4.310299557
100038347_at 7.994876138
100038358_at 4.300406414
100038371_at 3.776758053
100038392_at 4.071828723
100038398_at 3.905002964

Total number of rows: 17607

Table truncated, full table size 366 Kbytes.




Supplementary file Size Download File type/resource
GSM1697397_EA09031_86241_M430-2_23_DUODENUM_MGI_GENE-3.CEL.gz 3.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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