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Sample GSM547587 Query DataSets for GSM547587
Status Public on Aug 31, 2010
Title Skin Type III, Patient 23
Sample type RNA
 
Channel 1
Source name Skin Type III, Patient 23
Organism Homo sapiens
Characteristics phototypes: Type III
Extracted molecule total RNA
Extraction protocol Total RNA from fibroblats was prepared using RNAeasy kit (Qiagen, Valencia, CA).
Label cy3
Label protocol cDNA samples generated from RNA samples and purified before the coupling reaction were labeled with Cy3 (for fibroblast samples) or Cy5 (for reference RNA) mono-reactive dyes (GE Healthcare, Piscataway, NJ), and were hybridized simultaneously on an oligo-DNA chip (Hs-OperonV3.0-v1p24, p27, p31) overnight at 42°C.
 
Channel 2
Source name Universal Human Reference RNA
Organism Homo sapiens
Characteristics reference: Equal quantities of total RNA from each cell line (brain, breast, B-lymphocyte, cervix, liver, liposarcoma, macrophages, skin, testis, Y-lymphocyte) were pooled together. Provided by Stratagene (La Jolla, CA).
Extracted molecule total RNA
Extraction protocol Total RNA from fibroblats was prepared using RNAeasy kit (Qiagen, Valencia, CA).
Label cy5
Label protocol cDNA samples generated from RNA samples and purified before the coupling reaction were labeled with Cy3 (for fibroblast samples) or Cy5 (for reference RNA) mono-reactive dyes (GE Healthcare, Piscataway, NJ), and were hybridized simultaneously on an oligo-DNA chip (Hs-OperonV3.0-v1p24, p27, p31) overnight at 42°C.
 
 
Hybridization protocol Oligo-cDNA microarray hybridization was performed according to the National Cancer Institute in-house protocol. A universal human reference RNA (Stratagene, La Jolla, CA) was used as a control. cDNA samples generated from RNA samples and purified before the coupling reaction were labeled with Cy3 (for fibroblast samples) or Cy5 (for reference RNA) mono-reactive dyes (GE Healthcare, Piscataway, NJ), and were hybridized simultaneously on an oligo-DNA chip (Hs-OperonV3.0-v1p24, p27, p31) overnight at 42°C.
Scan protocol Scanned on GenePix 4000B. Images were quantified using GenePix Pro (version 5.0.1.24).
Data processing The data were processed by filtered 11,771 out of 36,288 spots with at least half of the corresponding intensity measures (CIMs) less than the mean of the background signal of the array plus three times the standard deviation of the background for further analysis. Data were then processed by subtracting background signals, conducting loess within-array and quantile between-array on the common reference channel normalization. One spot, Block 45, Column 18, Row 14, an empty well but passing the filtering criteria, was excluded from the data matrix.
 
Submission date May 27, 2010
Last update date Aug 31, 2010
Contact name Vincent Hearing
E-mail(s) hearingv@nih.gov
Organization name National Institutes of Health
Department National Cancer Institute
Lab Laboratory of Cell Biology
Street address Bldg 37 Rm 2132
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL3779
Series (1)
GSE22022 Microarray profiling of expression patterns of fibroblasts from different skin types

Data table header descriptions
ID_REF
VALUE loess within-array and quantile between-array normalized log2 ratio (sample/reference, i.e., cy3/cy5)

Data table
ID_REF VALUE
1718853_1 0.240310292
1718854_1 0.481850576
1718855_1 1.58438949
1718856_1 -0.755743934
1718857_1 0.823931096
1718858_1 -3.315818425
1718860_1 0.507552543
1718861_1 -0.369222576
1718862_1 0.388540374
1718863_1 1.657317671
1718864_1 -0.382914218
1718868_1 1.180293862
1718877_1 1.842054741
1718878_1 0.503765496
1718880_1 0.53059363
1718882_1 0.861687345
1718883_1 -0.662598983
1718885_1 0.910315598
1718888_1 0.588043821
1718890_1 0.947436105

Total number of rows: 24516

Table truncated, full table size 534 Kbytes.




Supplementary file Size Download File type/resource
GSM547587.gpr.gz 3.4 Mb (ftp)(http) GPR
Raw data provided as supplementary file
Processed data included within Sample table

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