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Sample GSM857184 Query DataSets for GSM857184
Status Public on Jan 06, 2012
Title db/+ mouse sample 335
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_335.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 5.991
100017_at 8.764
100019_at 8.727
100034251_at 13.12
100036521_at 9.969
100037258_at 11.24
100037278_at 8.045
100038570_at 9.386
100038635_at 4.557
100038887_at 12.395
100038959_at 8.677
100039027_at 4.814
100039094_at 4.904
100039235_at 6.756
100039282_at 3.132
100039284_at 7.894
100039307_at 6.674
100039332_at 4.836
100039359_at 5.996
100039495_at 7.889

Total number of rows: 15385

Table truncated, full table size 233 Kbytes.




Supplementary file Size Download File type/resource
GSM857184.CEL.gz 6.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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