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Sample GSM2385034 Query DataSets for GSM2385034
Status Public on Nov 06, 2018
Title ASD_115_22_06
Sample type RNA
 
Source name Peripheral blood from ASD patient
Organism Homo sapiens
Characteristics diagnosis: autism spectrum disorder (ASD)
tissue: whole blood
age: 16y
gender: female
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 18.29933241
2 5.221823386
3 5.052718081
4 10.12651501
5 5.339072715
6 5.339072715
7 5.500676443
8 6.594118009
9 6.642620074
10 7.141775554
11 8.572940025
12 9.409276939
13 8.32329194
14 5.500676443
15 5.167343166
16 5.371503044
17 11.8372209
18 9.424047867
19 7.541957438
20 10.30179351

Total number of rows: 62976

Table truncated, full table size 1090 Kbytes.




Supplementary file Size Download File type/resource
GSM2385034_ASD_115_22_06.txt.gz 3.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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