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Sample GSM189470 Query DataSets for GSM189470
Status Public on Nov 29, 2007
Title tunica muscularis, biological rep1
Sample type RNA
Source name BALB/c mice aged 6-9-days, small intestine
Organism Mus musculus
Characteristics The mucosa and submucosa were removed by peeling and the tunica muscularis of the entire jejunum and ileum was used.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated and purified using Trizol (Invitrogen, Carlsbad, CA) and the RNeasy Mini kit (Qiagen, Valencia, CA) respectively per manufacturers' instructions. RNA was quantified and its quality was tested by Agilent Bioanalyser (Agilent Technologies, Palo Alto, CA).
Label biotin
Label protocol Total RNA from each sample was used to prepare biotinylated target RNA, according to the manufacturers' instructions. Briefly, about 50 ng of total RNA was used to generate first strand cDNA by using a T7-linked oligo(dT) primer. After second-strand synthesis, in vitro transcription was performed with unlabelled ribonucleotides (Ambion, PN AM1333). A second round of cDNA synthesis was then performed with random primers, followed by in vitro transcription with biotinylated UTP and CTP resulting in a final yield of more than 40ug cRNA.
Hybridization protocol Target cDNA generated from each sample were then processed as per manufacturer's recommendation using an Affymetrix GeneChip 3000 System Spike controls were added to 15 µg fragmented cRNA before overnight hybridization. Arrays were then washed and stained with streptavidin-phycoerythrin.
Scan protocol The sample was scanned on an Affymetrix GeneChip 3000 system.
Description Gene expression data from tunica muscularis tissues
Data processing Analysis was performed using publicly available software Bioconductor. Simpleaffy was used to preprocess individual probe intensities from CEL files into expression values from which fold changes were derived using Limma. Robust MultiArray Analysis (RMA), which uses quantile normalization for cross-chip normalization, was used to preprocess the data.
Submission date May 15, 2007
Last update date Aug 28, 2018
Contact name Hui Chen
Organization name University of Nevada, Reno
Department Physiology and Cell Biology
Street address 1664 N Virginia St
City Reno
State/province NV
ZIP/Postal code 89557
Country USA
Platform ID GPL1261
Series (1)
GSE7809 Transcriptional expression of ICC-DMP and ICC-MY in murine small intestine
Reanalyzed by GSE119085

Data table header descriptions
VALUE RMA Signal Intensity

Data table
1415670_at 7.060906503 P 0.025002749
1415671_at 8.304382511 P 0.001641799
1415672_at 9.048223857 P 0.001641799
1415673_at 6.659574139 P 0.001641799
1415674_a_at 6.825580055 P 0.001641799
1415675_at 7.024062543 P 0.001641799
1415676_a_at 9.869052551 P 0.001641799
1415677_at 7.258737077 P 0.020230851
1415678_at 9.830567523 P 0.001641799
1415679_at 9.204496637 P 0.001641799
1415680_at 7.663393786 P 0.001641799
1415681_at 6.93094673 P 0.004889845
1415682_at 5.318072889 P 0.00807846
1415683_at 9.595862937 P 0.001641799
1415684_at 5.518101903 P 0.002180626
1415685_at 6.75191117 P 0.001641799
1415686_at 8.194247245 P 0.001641799
1415687_a_at 8.372771836 P 0.001641799
1415688_at 9.336836231 P 0.001641799
1415689_s_at 7.44179207 P 0.002180626

Total number of rows: 45101

Table truncated, full table size 1634 Kbytes.

Supplementary file Size Download File type/resource
GSM189470.CEL.gz 3.7 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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