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Sample GSM597477 Query DataSets for GSM597477
Status Public on Sep 24, 2010
Title non-progressive sural nerve, patient 9
Sample type RNA
 
Source name non-progressive DN sural nerve 52 weeks
Organism Homo sapiens
Characteristics tissue: sural nerve
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from a 1 cm segment of each sural nerve biopsy 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 from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.
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 HGU133Plus2_Hs_ENTREZG version 12. Cyber-T and ChipInspector (Genomatix, Germany) were used to analyze the expression data.
 
Submission date Sep 23, 2010
Last update date Sep 23, 2010
Contact name Junguk Hur
E-mail(s) junguk.hur@med.und.edu
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 GPL10526
Series (1)
GSE24290 Sural nerve of progressive and non-progressive diabetic neuropathy patients

Data table header descriptions
ID_REF
VALUE RMA normalized signal intensity

Data table
ID_REF VALUE
10000_at 90.2
10001_at 292.2
10002_at 20.5
10003_at 457.3
100048912_at 5.6
100049716_at 227.4
10004_at 117.2
10005_at 65.0
10006_at 469.3
10007_at 722.7
10008_at 26.8
100093630_at 1250.4
10009_at 123.8
1000_at 129.9
100101467_at 54.0
10010_at 202.3
100113377_at 66.5
100113407_at 492.4
10011_at 643.7
100124700_at 251.3

Total number of rows: 17726

Table truncated, full table size 250 Kbytes.




Supplementary file Size Download File type/resource
GSM597477.CEL.gz 8.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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