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Sample GSM130851 Query DataSets for GSM130851
Status Public on Sep 08, 2006
Title MAQC_BIO_1_sB3
Sample type RNA
 
Channel 1
Source name MAQC sample B, i.e., Ambion Human Brain Reference RNA (HBRR, Catalog #6050)
Organism Homo sapiens
Characteristics MAQC sample
Extracted molecule total RNA
Label Cy3
Label protocol Fluorescent-labeled DNA (Cy3 and Cy5-dCTP) was produced through Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described in detail (Guo, Y. et al. J. Virol. 79, 14392-14403, 2005). Briefly, double-stranded cDNA containing T7 RNA polymerase promoter sequence was synthesized with 5 ug of total RNA using Reverse Transcription System, RNase H, DNA polymerase I and T4 DNA polymerase, according to the manufacturer’s recommended protocol (Promega).
 
Channel 2
Source name MAQC sample B, i.e., Ambion Human Brain Reference RNA (HBRR, Catalog #6050)
Organism Homo sapiens
Characteristics MAQC sample
Extracted molecule total RNA
Label Cy5
Label protocol Fluorescent-labeled DNA (Cy3 and Cy5-dCTP) was produced through Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described in detail (Guo, Y. et al. J. Virol. 79, 14392-14403, 2005). Briefly, double-stranded cDNA containing T7 RNA polymerase promoter sequence was synthesized with 5 ug of total RNA using Reverse Transcription System, RNase H, DNA polymerase I and T4 DNA polymerase, according to the manufacturer’s recommended protocol (Promega).
 
 
Scan protocol Slides were scanned with a confocal LuxScan scanner (CapitalBio Corp.). For two-color microarrays, the scanning setting for the Cy3 and Cy5 channels was manually balanced by visual inspection of the external control spots. The data from the obtained images were extracted with SpotData software (CapitalBio Corp.).
Description Sample-pair convention: A (A/B, Cy3/Cy5), B (B/A, Cy3/Cy5), sA (A/A, Cy3/Cy5), sB (B/B, Cy3/Cy5). The human genome-wide long oligonucleotide microarray was constructed inhouse at CapitalBio Corporation, Beijing, China.
Data processing The data from the obtained images were extracted with SpotData software (CapitalBio Corp.). The raw data were submitted to MAQC and further normalized by using linear-scaling and LOWESS.
 
Submission date Aug 25, 2006
Last update date Sep 01, 2006
Contact name Leming Shi
E-mail(s) lemingshi@fudan.edu.cn
Phone +86-18616827008
Organization name Fudan University
Department School of Life Sciences
Lab Center for Pharmacogenomics
Street address 2005 Songhu Road
City Shanghai
ZIP/Postal code 200438
Country China
 
Platform ID GPL4187
Series (1)
GSE5350 MicroArray Quality Control (MAQC) Project

Data table header descriptions
ID_REF Manufacturer's 'Feature_id'
VALUE Ratio defined as CH1/CH2 (Cy3/Cy5)
CH1_Median Channel 1 median intensity (background subtracted and linear-scaled LOWESS normalized) (Cy3)
CH2_Median Channel 2 median intensity (background subtracted and linear-scaled LOWESS normalized) (Cy5)

Data table
ID_REF VALUE CH1_Median CH2_Median
1 1.0405 97526.4453125 93732.71875
2 0.9616 96831.1328125 100695.2421875
3 1.2084 16842.44921875 13937.88476562
4 6.6733 85039.4765625 12743.15234375
5
6 0.9802 804.86346436 821.12115479
7 0.8724 147695.515625 169289.1875
8 0.7842 62696.72265625 79946.6171875
9 0.9250 27519.1875 29751.81445312
10 0.8763 19921.3671875 22733.7734375
11 1.2050 74096.578125 61490.19921875
12 1.0389 254040.171875 244525.0625
13 1.1255 60572.03125 53819.30078125
14 0.9139 77230.8984375 84503.6484375
15 733.6037 189842.09375 258.78018188
16 1.3523 523.98059082 387.4697876
17 1.3129 355.79046631 271.00250244
18 1.0135 6401.14990234 6316.14404297
19 0.9434 1211.32507324 1283.96069336
20 0.9937 1363.11865234 1371.79394531

Total number of rows: 23232

Table truncated, full table size 862 Kbytes.




Supplementary file Size Download File type/resource
GSM130851_BIO_1_sB3.lsr.gz 1.7 Mb (ftp)(http) LSR

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