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Sample GSM1063418 Query DataSets for GSM1063418
Status Public on Jan 15, 2013
Title Brain_CC_3
Sample type RNA
Source name Somatic cell clone CC-3
Organism Mus musculus
Characteristics tissue: brain
gender: female
age: neonate
cell type: Somatic cell clone CC-3
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 (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
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
VALUE Normalized signal intensity minus bad spots

Data table
A_52_P81210 1085.553
A_52_P77106 72.99469
A_52_P677117 null
A_52_P675171 1683.693
A_52_P673458 null
A_52_P670095 null
A_52_P600547 906.7061
A_52_P580582 104.0225
A_52_P565559 239.5732
A_52_P534870 864.0934
A_52_P525107 4678.881
A_52_P523459 143.8921
A_52_P507214 88.3942
A_52_P496503 305.2113
A_52_P49250 247.9093
A_52_P491849 268.016
A_52_P49080 826.3196
A_52_P49014 66.4582
A_52_P468472 6480.267
A_52_P462366 225.7785

Total number of rows: 34140

Table truncated, full table size 696 Kbytes.

Supplementary file Size Download File type/resource
GSM1063418_US45102915_251486823118_S01_GE1-v1_91-BETA_1_3.txt.gz 7.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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