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Sample GSM892741 Query DataSets for GSM892741
Status Public on Sep 21, 2012
Title 2nd fraction of S series slicing
Sample type RNA
 
Source name 5 micron x 200 sagittal slices (1 mm width) of the brain, set 1
Organism Mus musculus
Characteristics strain: C57BL/6J
tissue: brain
gender: male
age: 8 weeks
section type: sagittal plane
mouse id: 1
Growth protocol Mice were grown in pathogen-free conditions.
Extracted molecule total RNA
Extraction protocol RNA was prepared using the Mag-max-96 for Microarrays Total RNA Isolation Kit (Ambion) following the manufacturer's recommendations of the spin column protocol. 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 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNeasy 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 (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 manufacturer's instructions. On completion of the fragmentation reaction, 250 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays 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 using the 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%).
Description S__02
Data processing The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Data were normalized using per chip: normalize to 50th percentile.
 
Submission date Mar 09, 2012
Last update date Sep 21, 2012
Contact name Yuko Okamura-Oho
E-mail(s) yoho-tky@umin.ac.jp
Organization name RIKEN
Street address 2-1, Hirosawa
City Wako-shi
State/province Saitama
ZIP/Postal code 351-0198
Country Japan
 
Platform ID GPL7202
Series (1)
GSE36408 Gene expression profiling of the whole mouse brain using transcriptome tomography

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
A_51_P108701 284.9182
A_51_P266695 4.6650076
A_51_P314264 67.096886
A_51_P425962 342.0773
A_51_P237076 178.49443
A_51_P276939 2.8635352
A_51_P377760 6.4285016
A_51_P296940 4.296207
A_52_P50107 33.96223
A_51_P481978 13.77931
A_52_P648203 5.8359523
A_52_P1092136 1.2451487
A_52_P139093 17.941517
A_51_P296975 1.2954006
A_51_P348672 15.037354
A_51_P513424 14.287012
A_52_P139097 76.59618
A_52_P674759 24.69286
A_51_P479786 2.9591038
A_51_P386189 91.22657

Total number of rows: 36558

Table truncated, full table size 826 Kbytes.




Supplementary file Size Download File type/resource
GSM892741_Processed-US14702386_251486810736_S01_GE1-v5_91_0806_1_1.txt.gz 1.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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