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Sample GSM545618 Query DataSets for GSM545618
Status Public on May 15, 2013
Title Patient 41T
Sample type RNA
 
Source name primary lung tumor
Organism Homo sapiens
Characteristics tissue: primary lung tumor
histology: SQ
stage: IIIA
sex: Male
age: 74 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 1085 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
E-mail(s) ycw5798@mail.ncku.edu.tw
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
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
PH_hs_0034221 3.5294108
PH_hs_0015259 3.7720604
PH_hs_0027756 3.3945944
PH_hs_0016855 9.747517
PH_hs_0032242 2.407078
PH_hs_0035253 3.2604384
PH_hs_0026012 8.202588
PH_hs_0012933 3.3945944
PH_hs_0024497 7.4372616
PH_hs_0015588 4.2480874
PH_hs_0012809 5.0159698
PH_hs_0016876 8.39086
PH_hs_0032244 3.1181233
PH_hs_0004792 9.114808
PH_hs_0037688 3.7720604
PH_hs_0034114 8.07499
PH_hs_0034570 3.1181233
PH_hs_0014268 0.5312326
PH_hs_0000369 2.6072738
PH_hs_0003283 0.5312326

Total number of rows: 30967

Table truncated, full table size 712 Kbytes.




Supplementary file Size Download File type/resource
GSM545618.gpr.gz 2.6 Mb (ftp)(http) GPR
Processed data included within Sample table

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