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Sample GSM773461 Query DataSets for GSM773461
Status Public on Nov 01, 2011
Title mouse_nerve
Sample type RNA
 
Source name Mouse, nerve cell
Organism Mus musculus
Characteristics strain: C57BL/6
cell type: nerve
Extracted molecule total RNA
Extraction protocol All RNAs are provided by Lonza. We extracted them accroding to their manuals.
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 (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 8x60k Oligo Microarrays (030829) 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 (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).
Description SAMPLE 3
Data processing The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 030829_D_F_20101021) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
 
Submission date Aug 04, 2011
Last update date Nov 01, 2011
Contact name Jun Sese
E-mail(s) sese.jun@aist.go.jp
Organization name National Institute of Advanced Industrial Science and Technology
Street address 2-4-7 Aomi
City Koto
State/province Tokyo
ZIP/Postal code 135-0064
Country Japan
 
Platform ID GPL14113
Series (2)
GSE31201 Inter-species array between human, rat and mouse
GSE31202 Gene expression levels with various artificial mutations and inter-species array

Data table header descriptions
ID_REF
VALUE Log2 normalized signal intensity

Data table
ID_REF VALUE
CPTH_G100077A 855.5136
CPTH_G10008A 3.780854
CPTH_G1000A 136.9901
CPTH_G10010A 4.135394
CPTH_G100149A 3.48583
CPTH_G10019A 3.636376
CPTH_G1001A 47.25877
CPTH_G10026A 3.133914
CPTH_G10027A 3.289945
CPTH_G10028A 29.28078
CPTH_G10029A 3.543616
CPTH_G1002A 44.05271
CPTH_G10034A 3.143291
CPTH_G10046A 4863.887
CPTH_G10047A 101.511
CPTH_G10055A 136.7996
CPTH_G100608A 3.275577
CPTH_G10070A 3.51258
CPTH_G100714A 3.341682
CPTH_G100715A 3.668208

Total number of rows: 59500

Table truncated, full table size 1256 Kbytes.




Supplementary file Size Download File type/resource
GSM773461_mouse_nerve.txt.gz 2.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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