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Sample GSM545656 Query DataSets for GSM545656
Status Public on May 15, 2013
Title Patient 176N
Sample type RNA
Source name primary normal lung tissue
Organism Homo sapiens
Characteristics tissue: primary normal lung tissue
sex: Male
age: 50 years
Extracted molecule total RNA
Extraction protocol Total RNA was prepared from tumors and normal lung tissues using TRIzol reagent (Invitrogen), and cleaned up RNA with RNeasy mini kit (Qiagen) and RNase-free DNase set (Qiagen).
Label Cy5
Label protocol 5 µg of total RNA was reverse-transcribed and amplified using MessageAmpTM aRNA Amplification Kit (Ambion). Indirect labeling the aa-UTP whereon by NHS-CyDye (Cy5, Amershan).
Hybridization protocol HOA v4.2 arrays (Phalanx Biotech Group, Taiwan) were pre-heat at 60℃ for 10 mins, rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, 10 µg Cy5-labeled aRNA was hybridize on HOA in the presentation of the Phalanx OneArray hybridization buffer.
Scan protocol The arrays were scanned by Axon GenePix 4000B scanner (635nm power 33 PMT 460; 532nm power 33, PMT 460) and quantify the fluoresence intensity.
Description Hybridization targets were prepared from total RNA and hybridized according to standard protocol using Phalanx Human OneArray chip (32,050 total features: 30968 human genome probes and 1123 experimental control probes).
Data processing All signal intensities was combined together and processed background subtraction by Microsoft Excel 9.0 software. Keep those probes that flags of GenePix have to be equal to 0 and the signal/noise ratio should be more than 5 for further Quantile normalization developed from Matlab 7.3.
Submission date May 20, 2010
Last update date May 16, 2013
Contact name Yi-Ching Wang
Phone +886-6-2353535
Organization name National Cheng Kung University
Department Department of Pharmacology, College of Medicine
Street address No.1, University Road, Tainan 70101, Taiwan, R. O. C.
City Tainan
ZIP/Postal code 70101
Country Taiwan
Platform ID GPL6254
Series (1)
GSE21933 Gene expression profiles of tumor and paired normal lung tissues from primary non-small cell lung cancer (NSCLC) patients in Taiwan.

Data table header descriptions
VALUE Normalized signal intensity

Data table
PH_hs_0034221 2.0038583
PH_hs_0015259 4.044455
PH_hs_0027756 4.521964
PH_hs_0016855 8.161188
PH_hs_0032242 2.0038583
PH_hs_0035253 3.2185738
PH_hs_0026012 9.099511
PH_hs_0012933 4.503085
PH_hs_0024497 10.016956
PH_hs_0015588 6.0957375
PH_hs_0012809 4.8894496
PH_hs_0016876 8.51031
PH_hs_0032244 2.6337028
PH_hs_0004792 10.162547
PH_hs_0037688 4.23044
PH_hs_0034114 8.374211
PH_hs_0034570 4.8290286
PH_hs_0014268 0.36006752
PH_hs_0000369 3.2185738
PH_hs_0003283 2.2653036

Total number of rows: 30967

Table truncated, full table size 713 Kbytes.

Supplementary file Size Download File type/resource
GSM545656.gpr.gz 2.7 Mb (ftp)(http) GPR
Processed data included within Sample table

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