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Sample GSM1892757 Query DataSets for GSM1892757
Status Public on Sep 25, 2015
Title Lung_Squamous_Carcinoma_Patient2
Sample type RNA
 
Source name Lung Squamous Carcinoma Tissue
Organism Homo sapiens
Characteristics tissue: Cancer tissue obtained from bronchoscopy
status: Mild-moderate dysplasia
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from frozen tissues using the TRIzol RNA isolation reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s specifications. RNA integrity was evaluated using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). If the RNA integrity number was greater than or equal to 6.5, the total RNA was purified using the RNeasy Mini Kit (Cat No.74106, Qiagen, Germany). The RNA concentration was determined with a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, Wilmington, USA).
Label Cy3
Label protocol CTP-cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Microarray-Based Gene Expression Analysis (Agilent, version 6.6) according to manufacturer's instructions, followed by RNeasy column purification (RNeasy Mini kit, QIAGEN). Dye incorporation and cRNA yield and quality were checked by spectrophotometry (Nanodrop ND1000, Labtech) and with the Agilent 2100 Bioanalyser.
 
Hybridization protocol 600 ng of CTP-Cy3-labelled cRNA (specific activity > 10.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 min in a reaction volume of 25 µl containing 25 x Agilent fragmentation buffer and 10 x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2 x Agilent hybridization buffer were added to the fragmentation mixture and hybridized to SurePrint G3 Human GE v2 8x60K (Agilent) for 17 h at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed 1 min at room temperature with GE Wash Buffer 1 (Agilent) and 1 min with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief passage in acetonitrile.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60k array slides: scan area was 61x21.6 mm, scan resolution 3 µm, dye channel was set to Green, Tiff file dynamic range was 20 bits and Green PMT was set to 100 %.
Description Gene expression of lung squamous carcinoma precancerous and cancer tissue
Data processing Normalized expression data were extracted with R package “limma” using cyclic loess method, and the ComBat algorithm was utilized to eliminate potential batch effects
 
Submission date Sep 24, 2015
Last update date Apr 23, 2018
Contact name Ning An
E-mail(s) nick_anning@sina.com
Phone 86-1087788409
Organization name Chinese academy of medical sciences
Street address NO.17 Pan Jiayuan Nan Li, Chao Yang District
City Beijing
ZIP/Postal code 100021
Country China
 
Platform ID GPL17077
Series (1)
GSE73402 Sixty-two lung squamous precancerous and cancer samples obtained from brochoscopy
Relations
Reanalyzed by GSE113533

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
A_23_P117082 0.022530079
A_33_P3246448 0.26186943
A_33_P3318220 0.1486783
A_33_P3236322 2.0725389
A_33_P3319925 0.28305626
A_21_P0000744 -0.515234
A_24_P215804 -0.9090309
A_23_P110167 0.72332144
A_33_P3211513 -0.33212948
A_23_P103349 -0.19721031
A_32_P61480 -0.43749332
A_33_P3788124 0.098677635
A_33_P3414202 0.18474293
A_33_P3316686 -0.6402292
A_33_P3300975 -1.3474393
A_33_P3263061 0.9449153
A_33_P3261373 -0.08188677
A_24_P278460 0.078193665
A_21_P0013109 0.16368961
A_21_P0014651 0.2156148

Total number of rows: 50524

Table truncated, full table size 1207 Kbytes.




Supplementary file Size Download File type/resource
GSM1892757_P058.txt.gz 3.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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