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Sample GSM2385001 Query DataSets for GSM2385001
Status Public on Nov 06, 2018
Title Con_056_10_06
Sample type RNA
 
Source name Peripheral blood from control subject
Organism Homo sapiens
Characteristics diagnosis: control
tissue: whole blood
age: 22y
gender: male
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from peripheral blood of participants by using the Paxgene Blood RNA System (QIAGEN, Tokyo, Japan) following the manufacture’s protocol with on-column DNase digestion.RNA quantity was measured using a Nano-drop ND-2000 spectrophotometer (Thermo Fisher Scientific, Yokohama, Japan). Qualities of RNA was determined by the Agilent 2100 Bioanalyzer (Agilent Technologies, Tokyo, Japan). RNA integrity number (RIN) values greater than 8 were used for subsequent analyses.
Label Cy3
Label protocol Total RNA (100 ng) was labeled with Cy3 using Low Input Quick Amp RNA Labeling kit, One-Color (Agilent Technologies) according to the manufacturer's instructions. Labelled cRNA were purified using an RNeasy mini kit (QIAGEN).. Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.
 
Hybridization protocol 600 ng of Cy3-labeled cRNA was fragmented and hybridized at 65 °C for 17 hours according to the manufacturer's instructions.
Scan protocol Slides were scanned on the Agilent Microarray scanner (G2565CA).
Data processing Data were extracted with Agilent Feature Extraction software version 11.0.1.1 (Agilent Technologies). Raw gene expression data were background corrected using the normexp method and normalized by the quantile method in Limma R package (Smyth et al.).
 
Submission date Nov 07, 2016
Last update date Nov 06, 2018
Contact name Ryo Kimura
E-mail(s) kimura.ryo.2w@kyoto-u.ac.jp
Organization name Kyoto University Graduate School of Medicine
Department Anatomy and Developmental Biology
Street address Yoshida-Konoe-cho
City Kyoto
ZIP/Postal code 606-8501
Country Japan
 
Platform ID GPL16699
Series (1)
GSE89594 Integrated network analysis reveals genotype-phenotype correlations in Williams syndrome

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
1 18.50814717
2 6.184600941
3 5.920498422
4 10.05155534
5 5.920498422
6 5.847343793
7 6.892390953
8 7.144679874
9 8.096137537
10 8.003619546
11 7.489203117
12 9.088533108
13 8.663499416
14 5.943936145
15 5.697470236
16 6.281846086
17 12.14852289
18 9.545456413
19 7.665974596
20 10.18861777

Total number of rows: 62976

Table truncated, full table size 1089 Kbytes.




Supplementary file Size Download File type/resource
GSM2385001_Con_056_10_06.txt.gz 3.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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