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Sample GSM857186 Query DataSets for GSM857186
Status Public on Jan 06, 2012
Title db/+ mouse sample 337
Sample type RNA
 
Source name 8 week db/+ mouse sciatic nerve
Organism Mus musculus
Characteristics strain: BKS
genotype/variation: db/+
age: 8 weeks
tissue: sciatic nerve
Treatment protocol N/A
Growth protocol N/A
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from sciatic nerve using a commercially available silica gel-based isolation protocol (RNeasy Mini Kit, QIAGEN Inc., Valencia, CA) including an on-column DNase digestion following the manufacturer's protocol. RNA quantity and quality was measured by microfluid electrophoresis using the RNA 6000 Pico LabChip® on a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
Label biotin
Label protocol Of the total RNA, 75 ng from each sample was amplified and biotin-labeled using the Ovation™ Biotin-RNA Amplification and Labeling System (NuGEN Technologies Inc., San Carlos, CA) according to the manufacturer’s protocol
 
Hybridization protocol Following Labeling, 4 ug of cDNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using the Affymetrix 3000 7G GeneChip Scanner with Autoloader.
Description Feldman_337.CEL
Gene expression data from 8 week db/+ mouse sciatic nerve
Data processing The Affymetrix CEL files were initially analyzed using a local version of the GenePattern genomic analysis platform from the Broad Institute. The samples were Robust Multi-array Average (RMA) normalized using the BrainArray Custom CDF version 12. Since the RNA amplification and hybridization was performed in two batches, normalized, log2 transformed expression values from the two batches of microarrays were adjusted for batch effect bias using the Distance Weighted Discrimination (DWD) batch effect correction method.
 
Submission date Jan 05, 2012
Last update date Jan 06, 2012
Contact name Manjusha Pande
E-mail(s) mpande@umich.edu
Organization name University of Michigan
Department BRCF
Lab Bioinformatics Core
Street address 2800 Plymouth Rd.
City Ann Arobr
ZIP/Postal code 48109
Country USA
 
Platform ID GPL9746
Series (1)
GSE34889 Molecular Mechanisms of Diabetic Neuropathy: A Transcriptional Profling Study of db/db Mouse Sciatic Nerve

Data table header descriptions
ID_REF
VALUE normalized, log2 transformed RMA signal

Data table
ID_REF VALUE
100009600_at 5.696
100017_at 8.743
100019_at 8.595
100034251_at 12.607
100036521_at 10.026
100037258_at 11.143
100037278_at 8.168
100038570_at 9.371
100038635_at 4.353
100038887_at 12.35
100038959_at 8.866
100039027_at 4.121
100039094_at 4.457
100039235_at 6.787
100039282_at 3.025
100039284_at 8.82
100039307_at 7.77
100039332_at 4.922
100039359_at 6.249
100039495_at 8.721

Total number of rows: 15385

Table truncated, full table size 233 Kbytes.




Supplementary file Size Download File type/resource
GSM857186.CEL.gz 6.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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