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Sample GSM1063419 Query DataSets for GSM1063419
Status Public on Jan 15, 2013
Title Brain_CC_4
Sample type RNA
 
Source name Somatic cell clone CC-4
Organism Mus musculus
Characteristics tissue: brain
gender: female
age: neonate
cell type: Somatic cell clone CC-4
genetic background: (C57BL/6 x DBA2) x 129/Sv
Extracted molecule total RNA
Extraction protocol RNA was prepared using the Trizol kit (Lifetech) following the manufacturer's recommendations. Total RNA was then clean-up by RNAeasy column purification (QIAGEN). RNA was quantified using a NanoDrop-1000 spectrophotometer.
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 kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
 
Hybridization protocol 1.5 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 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 Mouse Genome Oligo Microarrays (G4112A) 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 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100% and 10% (XDR)).
Description Gene expression of neonatal brain from cumulus cell derived clone mouse.
Data processing The scanned images were analyzed with Feature Extraction Software 9.5.3.1 (Agilent) using default parameters (protocol GE1-v1_91-BETA and Grid: 014868_D_20070207) to obtain background subtracted and spatially detrended Processed Signal intensities.
Signals below background in the process of normalization and analysis. Thus removed values were indicated as null. Omitted null data from the normalized data leaving 34,140 probes. Signal for duplicated probes were represented by the mean value of them.
 
Submission date Jan 14, 2013
Last update date Jan 18, 2013
Contact name Takashi Kohda
E-mail(s) tkohda.epgn@mri.tmd.ac.jp
Organization name Tokyo Medical and Dental University
Department Medical Research Institute
Lab Epigenetics
Street address 1-5-45 Yushima, Bunko-ku
City Tokyo
ZIP/Postal code 113-8510
Country Japan
 
Platform ID GPL7202
Series (1)
GSE43476 Genomic Reprogramming Errors Do Not Accumulate with Serial Recloning in the Mouse

Data table header descriptions
ID_REF
VALUE Normalized signal intensity minus bad spots

Data table
ID_REF VALUE
A_52_P81210 950.5278
A_52_P77106 71.58706
A_52_P677117 63.07939
A_52_P675171 1668.262
A_52_P673458 null
A_52_P670095 null
A_52_P600547 916.5885
A_52_P580582 97.66274
A_52_P565559 333.7249
A_52_P534870 916.2496
A_52_P525107 5171.989
A_52_P523459 153.56
A_52_P507214 84.67771
A_52_P496503 309.7822
A_52_P49250 280.5224
A_52_P491849 293.1791
A_52_P49080 966.7472
A_52_P49014 87.83727
A_52_P468472 6902.738
A_52_P462366 223.7583

Total number of rows: 34140

Table truncated, full table size 698 Kbytes.




Supplementary file Size Download File type/resource
GSM1063419_US45102915_251486823118_S01_GE1-v1_91-BETA_1_4.txt.gz 7.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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