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Sample GSM1820498 Query DataSets for GSM1820498
Status Public on Jul 12, 2016
Title SCN_ob/ob_ 5
Sample type RNA
Source name sciatic nerve, female, 26 week, diabetic
Organism Mus musculus
Characteristics gender: female
genotype/variation: ob/ob
tissue: sciatic nerve
Treatment protocol N/A
Growth protocol N/A
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from dorsal root ganglia and sciatic nerve biopsies using a commercially available kit (RNeasy Mini Kit; QIAGEN, Inc., Valencia, CA), including an on-column deoxyribonuclease digestion and following the manufacturer’s protocol. RNA quality and quantity were assessed by microfluid electrophoresis using an RNA 6000 Pico LabChip on a 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA).
Label biotin
Label protocol Biotinylated cDNA were prepared according to the Nugen Ovation V2 kit protocol from 75 ng total RNA (Ovation RNA Amplification System V2 Manual, 2007, NuGEN).
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 gene expression data
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 16 Entrez.
Submission date Jul 13, 2015
Last update date Jul 12, 2016
Contact name Junguk Hur
Organization name University of North Dakota
Department Biomedical Sciences
Street address 1301 N. Columbia Rd. Stop 9037
City Grand Forks
State/province ND
ZIP/Postal code 58202-9037
Country USA
Platform ID GPL16368
Series (1)
GSE70852 Dorsal root ganglia (DRG) and Sciatic nerve (SCN) in female BTBR ob/ob mice - diabetic peripheral neuropathy

Data table header descriptions
VALUE RMA signal - BrainArray Custom CDF v16 Entrez.

Data table
100008567_at 249.79
100009600_at 105.86
100012_at 10.36
100017_at 150.00
100019_at 229.40
100034251_at 838.40
100034739_at 15.03
100034748_at 32.58
100036520_at 94.85
100036521_at 279.29
100036523_at 26.72
100036768_at 31.83
100037258_at 734.14
100037262_at 30.89
100037278_at 98.83
100038347_at 216.93
100038358_at 20.71
100038371_at 91.80
100038392_at 46.74
100038398_at 28.33

Total number of rows: 17565

Table truncated, full table size 277 Kbytes.

Supplementary file Size Download File type/resource
GSM1820498_EF2011-60_SCN-obob.CEL.gz 6.3 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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