NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM424645 Query DataSets for GSM424645
Status Public on Nov 10, 2010
Title Peripheral mononuclear blood cells in patients with vasculitis 6
Sample type RNA
 
Channel 1
Source name Peripheral mononuclear blood cells from 16 healthy controls
Organism Homo sapiens
Characteristics disease status: healthy controls without any identified diseases
gender: 9 females and 7 males
age: avg 38.2
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 Cy3
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 (pooled sample from 16 healthy control patients) 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 3-CTP (Cy3-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 A552nm for Cy3-CTP with Agilent 2100 Bioanalyzer (Agilent Technologies).
 
Channel 2
Source name Peripheral blood cells from vasculitis patient 6
Organism Homo sapiens
Characteristics gender: female
age: 70
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 Before hybridization, 825ng labeled cRNA of each product was fragmented and mixed with control targets and hybridization buffer according to the manufacturer's protocol (Agilent Technologies). Hybridizations were done for approximately 17h at 65°C. The slides were washed according to the manufacturer's manual, and scanning of microarrays was performed with 5µm resolution using a DNA microarray laser scanner (Agilent Technologies).
Scan protocol The array was scanned using Agilent G2505B DNA microarray scanner.
Description Genes expressed in peripheral blood mononuclear cells from patients with vasculitis.
Data processing The image files were extracted using Agilent Feature Extraction software version 9.5.1 and LOWESS background subtraction and dye-normalization were used.
 
Submission date Jul 03, 2009
Last update date Nov 10, 2010
Contact name Daisuke Okuzaki
E-mail(s) dokuzaki@biken.osaka-u.ac.jp
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 GPL4133
Series (2)
GSE16945 Comparative transcription profiling of peripheral blood mononuclear cells from vasculitis patients
GSE18316 Genopal: a novel platform for focused microarray analysis

Data table header descriptions
ID_REF
VALUE Normalized signal intensity (Cy5/Cy3)
CH1_SIG_MEAN gProcessedSignal
CH1_BKD_MEAN gBGUsed
CH2_SIG_MEAN rProcessedSignal
CH2_BKD_MEAN rBGUsed

Data table
ID_REF VALUE CH1_SIG_MEAN CH1_BKD_MEAN CH2_SIG_MEAN CH2_BKD_MEAN
1 -2.17E-02 4.10E+05 66.1501 3.90E+05 59.9029
2 -2.93E-01 2.16E+01 66.3578 1.10E+01 59.8826
3 -2.14E-01 1.82E+01 66.5475 1.11E+01 59.8668
4 -4.34E-01 3.02E+01 66.7203 1.11E+01 59.8534
5 0.00E+00 1.22E+01 66.9091 1.13E+01 59.8505
6 -7.35E-01 6.07E+01 67.0912 1.12E+01 59.8458
7 -1.14E+00 1.55E+02 67.2608 1.11E+01 59.8436
8 -9.26E-01 9.47E+01 67.4146 1.12E+01 59.8551
9 -8.68E-01 8.34E+01 67.5704 1.13E+01 59.8736
10 -9.65E-01 1.27E+02 67.7264 1.37E+01 59.8988
11 -1.20E+00 1.81E+02 67.8761 1.13E+01 59.9291
12 2.23E-01 3.90E+03 68.0178 6.52E+03 59.9587
13 -7.47E-01 2.02E+02 68.1554 3.62E+01 59.9969
14 -1.89E-01 7.69E+02 68.2875 4.98E+02 60.0375
15 -4.13E-01 1.83E+02 68.412 7.07E+01 60.0799
16 -1.26E-01 4.70E+03 68.5311 3.51E+03 60.1232
17 -1.07E+00 2.05E+02 68.6477 1.73E+01 60.1781
18 -5.42E-01 2.41E+02 68.7566 6.92E+01 60.2373
19 1.26E-01 2.31E+04 68.8453 3.10E+04 60.2985
20 -9.36E-01 1.72E+02 68.9192 1.99E+01 60.3589

Total number of rows: 45015

Table truncated, full table size 2149 Kbytes.




Supplementary file Size Download File type/resource
GSM424645.txt.gz 12.8 Mb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap