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Sample GSM2711259 Query DataSets for GSM2711259
Status Public on Dec 01, 2017
Title ISL-treated (Cy5)/Control (Cy3)-LNCaP
Sample type RNA
 
Channel 1
Source name ISL-treated LNCaP cells
Organism Homo sapiens
Characteristics cell line: LNCaP Prostate Cancer Cell Line
treatment: ISL
Treatment protocol LNCaP cells and PC-3 cells were seeded into 25 cm2 flask at a density of 5×104 cells per flask. After 24h of incubation, cells were treated with 25 μM ISL or 0.025% DMSO as control for 48h.
Growth protocol LNCaP cells or PC-3 cells were maintained in RPMI-1640 (Hyclone, USA) supplemented with 10% FBS (Hyclone, USA), 1% penicillin and streptomycin at 37°C in a humidified incubator containing 5% CO2.
Extracted molecule total RNA
Extraction protocol After treatment, cells were harvested and washed with cold PBS. Total RNA was extracted using Trizol Reagent (Invitrogen, USA) according to the manufacturer's instrctions and stored at -80°C waiting for quality test and microarray analysis. The quality test and microarray experiment were performed by CapitlBio Corporation (Beijing, China). Total RNA was purified using NucleoSpin RNA clean-up kit (MACHEREY-NAGEL, Germany) and quantified by a spectrophotometer. The quality of samples were tested through electrophoresis on gel containing formaldehyde. Samples passing the qualifty test were allowed to step into the next stage of the experiment.
Label Cy5
Label protocol The labeling process was performed by using Jingxin cRNA Amplification and Labeling Kit according to the manufacture's instructions.
 
Channel 2
Source name Control LNCaP cells
Organism Homo sapiens
Characteristics cell line: LNCaP Prostate Cancer Cell Line
treatment: Control (untreated)
Treatment protocol LNCaP cells and PC-3 cells were seeded into 25 cm2 flask at a density of 5×104 cells per flask. After 24h of incubation, cells were treated with 25 μM ISL or 0.025% DMSO as control for 48h.
Growth protocol LNCaP cells or PC-3 cells were maintained in RPMI-1640 (Hyclone, USA) supplemented with 10% FBS (Hyclone, USA), 1% penicillin and streptomycin at 37°C in a humidified incubator containing 5% CO2.
Extracted molecule total RNA
Extraction protocol After treatment, cells were harvested and washed with cold PBS. Total RNA was extracted using Trizol Reagent (Invitrogen, USA) according to the manufacturer's instrctions and stored at -80°C waiting for quality test and microarray analysis. The quality test and microarray experiment were performed by CapitlBio Corporation (Beijing, China). Total RNA was purified using NucleoSpin RNA clean-up kit (MACHEREY-NAGEL, Germany) and quantified by a spectrophotometer. The quality of samples were tested through electrophoresis on gel containing formaldehyde. Samples passing the qualifty test were allowed to step into the next stage of the experiment.
Label Cy3
Label protocol The labeling process was performed by using Jingxin cRNA Amplification and Labeling Kit according to the manufacture's instructions.
 
 
Hybridization protocol Labeled DNA was hybridized in 2X GEx Hyb Buffer (HI-RPM) containing 25% formamide at 45°C overnight. After hybridization, microarrays were washed sequentially.
Scan protocol Microarrays were scanned on an Agilent G2565CA Microarray Scanner.
Description single sample, using qRT-PCR to validate the microarray result
Data processing Agilent Feature Extraction Software was used for image quantification, background subtraction and LOWESS mormalization.
 
Submission date Jul 19, 2017
Last update date Jan 23, 2018
Contact name Biyan Zhang
E-mail(s) zhang_bi_yan@hotmail.com
Organization name Shanghai University of Traditional Chinese Medicine
Department School of Basic Medicine
Street address 1200 Cai Lun Road, Pudong District
City Shanghai
State/province Shanghai
ZIP/Postal code 201203
Country China
 
Platform ID GPL17077
Series (1)
GSE101640 Human Prostate Cancer Cells: ISL-treated cells vs. Control

Data table header descriptions
ID_REF
VALUE Normalized log2 ratio (Cy5/Cy3) representing treated/control

Data table
ID_REF VALUE
A_23_P117082 -0.4822263
A_33_P3246448
A_33_P3318220
A_33_P3236322 0.022212861
A_33_P3319925
A_21_P0000509 0.5390072
A_21_P0000744 -0.03976071
A_24_P215804 -1.2161207
A_23_P110167 0.3654108
A_33_P3211513 0.11553474
A_23_P103349
A_32_P61480
A_33_P3788124
A_33_P3414202 0.6476726
A_33_P3316686 0.94674206
A_33_P3300975 -0.1791152
A_33_P3263061 0.46329126
A_33_P3261373
A_24_P278460 0.4228419
A_21_P0013109

Total number of rows: 50737

Table truncated, full table size 1011 Kbytes.




Supplementary file Size Download File type/resource
GSM2711259_LNCaP.txt.gz 6.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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