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Sample GSM400940 Query DataSets for GSM400940
Status Public on Aug 30, 2015
Title cecumdead_28days_1
Sample type RNA
 
Source name cecum,epithelial cell,dead,28days,1
Organism Mus musculus
Characteristics agent: dead, 28days
tissue: cecal epithelial cell
gender: female
age: 10-20y
Treatment protocol GB mouse was prepared from GF mouse by live or dead BbrY. Cecal epithelial cells were collected 3 days or 28 days after live or dead BbrY association. Cecal epithelial cells were released by incubation with HANKS including 4 mM EDTA and 10 mM HEPES at 37 °C and collected by centrifugation after being washed with PBS and filtrated with a filter (100 mesh). The collected epithelial cells were treated with TRI-zol reagents and stored at -80 °C.
Extracted molecule total RNA
Extraction protocol RNA was prepared using the Chloroform and isopropanol and DNase treatment at 37 °C. The total RNA was extracted from TRI-zol reagent buffer of cecal epithelial cells. RNA was quantified using the spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from total RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions. Dye incorporation and cRNA yield were checked with the Spectrophotometer.
 
Hybridization protocol 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60 °C for 30 minutes in a reaction volume of 55 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Microarrays (G4122F) for 17 hours at 65 °C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 °C GE Wash buffer 2 (Agilent) and 1 minute at room temperature acetonitorile.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDRHi 100% and XDRLo 10%).
Description Gene expression in ex-GF mouse 28days after dead BbrY association
Data processing The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_91 and Grid: 014868_D_20060807) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
 
Submission date May 08, 2009
Last update date Aug 30, 2015
Contact name tatsuichiro shima
E-mail(s) tatsuichiro_shima@yahoo.co.jp
Phone +81-42-577-8952
Organization name Yakult central institute for microbiological research
Department basic research
Lab intestinal function research
Street address izumi5-11
City kunitachi-si
State/province Tokyo
ZIP/Postal code 1860086
Country Japan
 
Platform ID GPL4134
Series (1)
GSE16021 The difference of gene expression for live or dead BbrY associated mice.

Data table header descriptions
ID_REF
VALUE processed Cy3 signal intensity

Data table
ID_REF VALUE
1 3.511022e+004
2 2.258979e+000
3 2.283449e+000
4 2.307423e+000
5 2.329313e+000
6 2.350185e+000
7 2.369678e+000
8 2.387450e+000
9 2.404271e+000
10 2.419837e+000
11 2.433601e+000
12 2.446355e+000
13 1.968829e+001
14 6.718009e+000
15 3.781548e+001
16 3.387275e+001
18 3.426917e+000
19 3.863011e+000
20 2.502081e+000
21 1.785518e+001

Total number of rows: 45018

Table truncated, full table size 868 Kbytes.




Supplementary file Size Download File type/resource
GSM400940.txt.gz 1.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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