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Sample GSM189465 Query DataSets for GSM189465
Status Public on Nov 29, 2007
Title ICC-DMP, biological rep2
Sample type RNA
 
Source name BALB/c mice aged 6-9-days, small intestine
Organism Mus musculus
Characteristics ICC-DMP cells were isolated from the tunica muscularis tissues by fluorescence-activated cell sorting .
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 ICC-DMP cells
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
Relations
Reanalyzed by GSE119085

Data table header descriptions
ID_REF
VALUE RMA Signal Intensity
ABS_CALL
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
1415670_at 6.996082546 P 0.002875125
1415671_at 7.786978134 P 0.002180626
1415672_at 11.57301431 P 0.001641799
1415673_at 7.050774339 P 0.002180626
1415674_a_at 8.008468733 P 0.001641799
1415675_at 7.501254671 P 0.001641799
1415676_a_at 10.25423529 P 0.001641799
1415677_at 7.351996055 P 0.002180626
1415678_at 11.27132017 P 0.001641799
1415679_at 10.05965002 P 0.002180626
1415680_at 8.16800085 P 0.001641799
1415681_at 7.086835221 P 0.002875125
1415682_at 5.393739676 P 0.010271902
1415683_at 10.09414957 P 0.001641799
1415684_at 5.158867065 P 0.002180626
1415685_at 7.123011285 P 0.001641799
1415686_at 8.690732269 P 0.001641799
1415687_a_at 9.804301928 P 0.001641799
1415688_at 10.06456418 P 0.001641799
1415689_s_at 8.229492576 P 0.001641799

Total number of rows: 45101

Table truncated, full table size 1634 Kbytes.




Supplementary file Size Download File type/resource
GSM189465.CEL.gz 3.2 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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