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Sample GSM206948 Query DataSets for GSM206948
Status Public on Oct 10, 2007
Title 14 weeks after first infliximab injection (14-14w-0)
Sample type RNA
 
Channel 1
Source name 14 weeks after first infliximab injection
Organism Homo sapiens
Characteristics Gender: female, Age: 60 years, ACR score at 14 weeks after first infliximab injection: 0%
Extracted molecule total RNA
Extraction protocol The blood (2.5 ml x 2 tubes) was drawn using PAXgene tubes (QIAGEN, Hilden, Germany). The total RNA extraction and purification were carried out according to the manufacturer’s protocol.
Label Cy5
Label protocol Then total RNA (1 mg) from patients was transcribed and amplified to produce amplified sample RNA (aRNA) using the MessageAmp aRNA kit according to the manufacturer’s instructions. Next, an external control RNA mixture (LD, GP, and RL) was added to both the sample and reference aRNA (9 mg each). These mixed sample and reference aRNA were labeled using SuperScript II kit (Invitrogen, Carlsbad, CA) with random hexamer (TaKaRa, Kyoto, Japan) with Cy3-dUTP and Cy5-dUTP (PerkinElmer, Boston, MA), respectively.
 
Channel 2
Source name Reference RNA
Organism Homo sapiens
Characteristics healthy volunteers
Extracted molecule total RNA
Extraction protocol The blood (2.5 ml x 2 tubes) was drawn using PAXgene tubes (QIAGEN, Hilden, Germany). The total RNA extraction and purification were carried out according to the manufacturer’s protocol.
Label Cy3
Label protocol Then total RNA (1 mg) from patients was transcribed and amplified to produce amplified sample RNA (aRNA) using the MessageAmp aRNA kit according to the manufacturer’s instructions. Next, an external control RNA mixture (LD, GP, and RL) was added to both the sample and reference aRNA (9 mg each). These mixed sample and reference aRNA were labeled using SuperScript II kit (Invitrogen, Carlsbad, CA) with random hexamer (TaKaRa, Kyoto, Japan) with Cy3-dUTP and Cy5-dUTP (PerkinElmer, Boston, MA), respectively.
 
 
Hybridization protocol Competitive hybridization of Cy3-labeled reference and Cy5-labeled sample cDNA on the microarray was carried out according to Brown and Yanofsky[10] with chamber systems (Agilent Technologies, Palo Alto, CA).
Scan protocol Slides were scanned five times with five different power ranges using ScanArray 5000 (PerkinElmer, Boston, MA).
Description no additional information
Data processing The data was converted from tif image data to signal using ImaGene software (BioDiscovery, El Segundo, CA) for further statistical analysis. Five file data of each four spot data corresponding each gene were merged to establish the single representative data for each gene (Patent pending: PCT/JP03/06677).
 
Submission date Jul 02, 2007
Last update date Aug 14, 2011
Contact name Tsutomu Takeuchi
Organization name Saitama Medical University
Department Department of Internal Medicine
Lab Division of Rheumatology/Clinical Immunology
Street address 1981 Tsujido-machi, Kamoda
City Kawagoe-shi, Saitama
ZIP/Postal code 350-8550
Country Japan
 
Platform ID GPL5460
Series (1)
GSE8350 mRNA expression profile in peripheral blood cells of RA patients following treatment with an anti-TNFa mAb, infliximab

Data table header descriptions
ID_REF
VALUE The Cy5 (patient sample)/Cy3 (reference sample) ratio of each mRNA signal was calculated for further analysis. The global Lowess normalization method was also applied before ratio calculation.

Data table
ID_REF VALUE
1 0.666675973
2 0.566742934
3 0.711888237
4 0.697426049
5 1.350303412
6 0.635199538
7 1.365287876
8 0.702775811
9 1.068436333
10 0.527738933
11 0.706979567
12 0.995078681
13 0.82658682
14 1.410782531
15 0.794085927
16 0.933625287
17 0.727812528
18 0.877980387
19 0.755703636
20 0.705244171

Total number of rows: 776

Table truncated, full table size 11 Kbytes.




Supplementary file Size Download File type/resource
GSM206948.txt.gz 23.6 Kb (ftp)(http) TXT
Processed data included within Sample table

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