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Sample GSM1207779 Query DataSets for GSM1207779
Status Public on Sep 17, 2013
Title muscle Smad4KO 2 denervated 14 days
Sample type RNA
Source name Gastrocnemius muscle denervated 14 days, Smad4 KO mouse
Organism Mus musculus
Characteristics tissue: whole Gastrocnemius
gender: adult male
strain: CD1
Extracted molecule total RNA
Extraction protocol Total RNA was prepared from Gastrocnemius muscles using TRIzol (Life Technologies) following the manufacturer's recommendations.Then a clean-up step and an on-column DNase I treatment were performed using Rneasy Fibrous Tissue Mini Kit (QIAGEN). RNA was quantified using a NanoDrop-1000 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 1 ug RNA using the One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
Hybridization protocol 1.65 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 μl of 2x GEx Hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo 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 at 37°C with GE Wash buffer 2 (Agilent), then dried.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5μm, Dye channel is set to Green and Green PMT is set to 100%).
Description Gene expression after 14 days of denervation
Data processing The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 014868_D_20070820) to obtain background subtracted and spatially detrended Processed Signal intensities.
Submission date Aug 13, 2013
Last update date Sep 17, 2013
Contact name Marco Sandri
Organization name VIMM (Venetian Institute of Molecular Biology)
Street address via Orus,2
City Padua
ZIP/Postal code 35129
Country Italy
Platform ID GPL7202
Series (1)
GSE49826 Gene expression profiling on innervated and denervated muscles of Smad4 KO and control mice.

Data table header descriptions
VALUE Normalized signal intensity (quantile normalization)

Data table
GE_BrightCorner 5033.422619
DarkCorner 7.222575758
A_52_P616356 3.499166667
A_52_P580582 8.278625
A_52_P403405 22.94166667
A_52_P819156 29.50416667
A_51_P331831 47.2625
A_51_P430630 3.5175
A_52_P502357 3.5175
A_52_P299964 3.5175
A_51_P356389 3.5175
A_52_P684402 75.61666667
A_51_P414208 3.5175
A_51_P280918 414.9166667
A_52_P613688 14.675
A_52_P258194 9.392083333
A_52_P229271 13.91666667
A_52_P214630 217.5
A_52_P579519 239.4166667
A_52_P979997 3.5975

Total number of rows: 41267

Table truncated, full table size 927 Kbytes.

Supplementary file Size Download File type/resource
GSM1207779_US22502723_251486835374_S01_GE1_107_Sep09_1_4.txt.gz 7.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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