|
| Status |
Public on Nov 27, 2012 |
| Title |
Whole_Blood_38 |
| Sample type |
RNA |
| |
|
| Source name |
Peripheral blood
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: whole blood
gender: female
age: 46
physical status: healthy
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Venous blood was collected between 1100 and 1200 h in PAXgene tubes (Qiagen, Valencia) from each subject and was incubated at room temperature for 24 h for RNA stabilization. RNA was extracted from whole blood according to the manufacturer's guidelines by using the PAXgene Blood RNA System Kit (PreAnalytix GmbH, Hombrechtikon, Switzerland). The extracted RNA was quantified by optical density readings at A260nm by using the NanoDrop ND-1000 (Thermo Scientific, Rockford) and agrose gel electrophoresis.
|
| Label |
biotin
|
| Label protocol |
After cDNA synthesis from total RNA, cyanine-3 (Cy3) labeled cRNA was prepared using transcribed using T7 RNA polymerase.
|
| |
|
| Hybridization protocol |
Cy3-labeled cRNA was hybridized to Agilent Human Genome 4 x 44 K arrays (Agilent Technologies) according to the manufacturer's instructions.
|
| Scan protocol |
Arrays were scanned by a DNA Microarray Scanner (Agilent G2505C). Microarray images were analyzed with Agilent Feature Extraction software.
|
| Description |
S1150
|
| Data processing |
Microarray images were analyzed with Agilent Feature Extraction software.
Raw signal data for each of the 3 independent samples were analyzed separately by the GeneSpring GX software (Agilent Technologies). Data were filtered according to the expression level for quality control to eliminate genes that were below the 20th percentile threshold. The expression value of each gene was normalized to the median expression value of all genes in each chip. A total of 30,465 probes were included in the analysis.
|
| |
|
| Submission date |
Nov 12, 2012 |
| Last update date |
Nov 27, 2012 |
| Contact name |
Daimei Sasayama |
| Organization name |
National Center of Neurology and Psychiatry
|
| Street address |
4-1-1 Ogawahigashi-machi
|
| City |
Kodaira |
| ZIP/Postal code |
187-8551 |
| Country |
Japan |
| |
|
| Platform ID |
GPL6480 |
| Series (2) |
| GSE42228 |
An eQTL study in the Japanese population [gene expression_2] |
| GSE42488 |
Identification of single nucleotide polymorphisms regulating peripheral blood mRNA expression with genome-wide significance: an eQTL study in the Japanese population |
|
