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Sample GSM455889 Query DataSets for GSM455889
Status Public on Nov 10, 2010
Title PBMCs from vasculitis patients 2
Sample type RNA
Source name Peripheral blood cells from vasculitis patient 2
Organism Homo sapiens
Characteristics gender: female
age: 27
disease status: vasculitis
Extracted molecule total RNA
Extraction protocol Peripheral blood was collected directly into PAXGene tubes (Qiagen, Valencia, CA) and stored at -80℃ until extraction. Total RNA from mononuclear cells was extracted using PAXGene Blood RNA kit with the optimal on-column DNase digestion according to the manufacturer's instructions.
Label Cy5
Label protocol RNA labeling was performed with a Fluorescent Linear Amplification Kit (Agilent Technologies). In brief, cDNA was reverse transcribed from 500ng of total RNA (derived from vasculitis patients 1 with an oligo-dT-T7 promoter primer and MMLV-RT. Second strand synthesis was carried out with random hexamers. Fluorescent antisense cRNA was synthesized with cyanine 5-CTP (Cy5-CTP) and T7 polymerase. The fluorescent-labeled antisense cRNA was purified with RNeasy columns (Qiagen) according to manufacturer's protocols and resuspended in water. The purified products were quantified at A650nm for Cy5-CTP with Agilent 2100 Bioanalyzer (Agilent Technologies).
Hybridization protocol Briefly, 1125 ng labeled cRNA was fragmented according to the manufacturer's protocol (Agilent Technologies), was suspended in a hybridization buffer containing 0.12 M Tris-HCl (pH 7.5), 0.12 M NaCl, and 0.05% Tween 20. The hybridization mixture was heated to 94°C for 2 min, then cooled to 37°C and injected into a hybridization chamber (Mitsubishi Rayon). Hybridization was carried out at 65°C for 16 hr. Microarrays were washed by soaking twice in 0.12 M Tris-HCl (pH 7.5), 0.12 M NaCl, 0.05% and Tween 20 at 65°C for 20 min, then once in 0.12 M Tris-HCl (pH 7.5), 0.12 M NaCl at 65°C for 10 min.
Scan protocol Microarray was scanned and the image was captured using a cooled charge-coupled device (CCD)-type Microarray Image Analyzer equipped with multibeam excitation technology (Yokogawa Electric Co., Tokyo, Japan).
Description Genes expressed in peripheral blood mononuclear cells from patients with vasculitis.
Data processing Data analysis with background subtraction and normalization to alpha-tubulin intensity was conducted using the GeneSpring GX software version 10.0.2, according to the manufacturer’s protocol (Agilent Technologies).
Submission date Sep 24, 2009
Last update date Nov 10, 2010
Contact name Daisuke Okuzaki
Phone +81-6-6879-4935
Organization name Osaka univ.
Department Immunology Frontier Research Center
Lab Human Immunology (Single Cell Genomics)
Street address Yamadaoka 3-1
City Suita
State/province Osaka
ZIP/Postal code 565-0871
Country Japan
Platform ID GPL9283
Series (2)
GSE18247 Focused transcription profiling of peripheral blood mononuclear cells from vasculitis patients
GSE18316 Genopal: a novel platform for focused microarray analysis

Data table header descriptions
VALUE Alpha-tubulin scaled normalized signal intensity

Data table
1 11.00
2 201.00
3 37.30
4 5.19
5 17.90
6 10.50
7 101.00
8 8.71
9 6.18
10 25.00
11 38.40
12 11.00
13 17.00
14 9.75
15 6.32
16 19.70
17 7.69
18 8.06
19 18.60
20 26.20

Total number of rows: 216

Table truncated, full table size 1 Kbytes.

Supplementary file Size Download File type/resource
GSM455889_technical_replicate_extract1.txt.gz 21.1 Kb (ftp)(http) TXT
GSM455889_technical_replicate_extract2.txt.gz 21.0 Kb (ftp)(http) TXT
GSM455889_technical_replicate_extract3.txt.gz 21.0 Kb (ftp)(http) TXT
GSM455889_technical_replicate_extract4.txt.gz 21.0 Kb (ftp)(http) TXT
Processed data included within Sample table

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