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Sample GSM547580 Query DataSets for GSM547580
Status Public on Aug 31, 2010
Title Skin Type I, Patient 12
Sample type RNA
 
Channel 1
Source name Skin Type I, Patient 12
Organism Homo sapiens
Characteristics phototypes: Type I
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 0.234659339
1718854_1 3.402011154
1718855_1 2.307130077
1718856_1 -1.018258627
1718857_1 1.320261488
1718858_1 1.891313435
1718860_1 2.854136023
1718861_1 1.667581176
1718862_1 2.894930708
1718863_1 2.002751368
1718864_1 0.841820602
1718868_1 1.365744371
1718877_1 1.697683902
1718878_1 1.385711903
1718880_1 1.060825498
1718882_1 -0.063429974
1718883_1 -1.528605511
1718885_1 1.132214275
1718888_1 0.882856785
1718890_1 0.953146198

Total number of rows: 24516

Table truncated, full table size 536 Kbytes.




Supplementary file Size Download File type/resource
GSM547580.gpr.gz 3.3 Mb (ftp)(http) GPR
Raw data provided as supplementary file
Processed data included within Sample table

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