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Sample GSM862439 Query DataSets for GSM862439
Status Public on Aug 01, 2013
Title CRF sham
Sample type RNA
Source name liver, sham-operated
Organism Mus musculus
Characteristics background strain: ICR
operation: sham-operated
tissue: liver
Treatment protocol 5/6Nxs were generated by the ablation of 2/3 of the right kidney and enucleation of the left kidney 1 week later.
Growth protocol 5/6 nephrectomized mice and sham-operated mice aged 4 to 16 weeks were housed under a 12-h light/dark cycle at room temperature 24 ± 1°C and humidity 60 ± 10% with food and water available ad libitum.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using theTRIzol .
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (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 1.5 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) 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), then dried immediately by brief centrifugation.
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 10um, Dye channel is set to Green and Green PMT is set to 100%).
Data processing The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
Submission date Jan 17, 2012
Last update date Aug 01, 2013
Contact name naoya matsunaga
Organization name kyushu university
Street address maidashi 3-1-1, higashi-ku
City fukuoka
ZIP/Postal code 8128582
Country Japan
Platform ID GPL11202
Series (2)
GSE35135 5/6 nephrectomy (5/6Nx) effect on the liver
GSE35136 5/6 nephrectomy (5/6Nx) effect on the brain and liver

Data table header descriptions
VALUE quantile normalized signal (non-log scaled) and ABS CALL.

Data table
A_55_P2116608 4.1133315 A
A_55_P2073489 134.749005 P
A_52_P229709 1566.9015 P
A_55_P2092526 1020.30345 P
A_55_P2048358 8.2338895 A
A_55_P2109122 11683.789 P
A_55_P2032147 38.216015 P
A_55_P1985351 14.695905 A
A_55_P2145838 4.040453 A
A_51_P163444 3848.624095 P
A_55_P2166688 1218.797 P
A_55_P2230663 4.4981915 A
A_55_P2195172 5.1471865 A
A_55_P1953663 3.8902865 A
A_55_P2135730 5.2931815 A
A_51_P174143 3.9415705 A
A_51_P419971 4332.86 P
A_55_P1967880 4372.5705 P
A_55_P2364315 208.66535 P
A_51_P154780 20.03539287 A

Total number of rows: 39429

Table truncated, full table size 970 Kbytes.

Supplementary file Size Download File type/resource
GSM862439_US22502696_252665510327_S01_GE1-v5_95_Feb07_1_3.txt.gz 9.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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