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Sample GSM1333954 Query DataSets for GSM1333954
Status Public on Mar 25, 2014
Title E11.5 mouse intestine
Sample type RNA
Source name mouse intestine E11.5
Organism Mus musculus
Characteristics tissue: intestine
stain: ICR
Treatment protocol Male and female mice were mated and the day of identification of a vaginal plug was E0.5. After 11days, mouse embryos were collected as E11.5.
Growth protocol ICR mouse were harbored following the guidelines of the National Institute of Advanced Industrial Science and Technology Animal Experiment Committee.
Extracted molecule total RNA
Extraction protocol The primordium stomach was dissected from mouse embryo at E11.5. Total RNA was isolated from stomach using the ‘RNeasy micro kit’ (Quiagen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer.
Label Cy3
Label protocol RNA was labeled using the ‘Agilent Low Input Quick Amp Kit’ (Agilent Technologies) following the manufacturer’s protocol. Cy3-labeled cRNA was purified with the RNeasy kit (Qiagen). Dye incorporation was assessed with the NanoDrop-1000 Spectrophotometer.
Hybridization protocol 1.65 ug of Cy3-labelled 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 Oligo Microarrays (G4122F) for 18 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), 1 minute with 37°C GE Wash buffer 2 (Agilent), and 30 second at room temperature with acetonitrile, then dried immediately.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 1x44k array slides.
Data processing The scanned images were analyzed with Feature Extraction Software 10. 5 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 014868_D_20070820) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non positive and significant, and Feature Non above background outliers were excluded.
Submission date Feb 25, 2014
Last update date Mar 25, 2014
Contact name Mari Sekine
Organization name The University of Tsukuba
Department Graduate School of Life and Environmental Sciences
Street address 1-1-1 Tennoudai
City Tsukuba
ZIP/Postal code 305-8577
Country Japan
Platform ID GPL7202
Series (1)
GSE55312 Transcription profile of primordium gut organs

Data table header descriptions
VALUE Normalized log2 signal intensity

Data table
A_52_P616356 -8.526453
A_52_P580582 -4.9004917
A_52_P403405 -4.2410583
A_52_P819156 -6.7740574
A_51_P331831 0.6483841
A_51_P430630 -6.5575223
A_52_P502357 -8.051258
A_52_P299964 -3.6340165
A_51_P356389 -6.3073997
A_52_P684402 -0.5305128
A_51_P414208 -6.2806196
A_51_P280918 0.17723179
A_52_P613688 -3.229025
A_52_P258194 -0.58183575
A_52_P229271 -2.9270377
A_52_P214630 -0.69911575
A_52_P579519 -2.5804343
A_52_P979997 -6.502557
A_52_P453864 -6.064167
A_52_P655842 -2.7752128

Total number of rows: 41265

Table truncated, full table size 941 Kbytes.

Supplementary file Size Download File type/resource
GSM1333954_1_e11.5_int.txt.gz 2.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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