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Sample GSM2462177 Query DataSets for GSM2462177
Status Public on Jul 24, 2017
Title MDAH MI-res1
Sample type RNA
 
Source name Epithelial Ovarian Carcinoma cells treated with platinum
Organism Homo sapiens
Characteristics tissue: ovarian cell line
histotype: endometrioid
Treatment protocol not applicable
Growth protocol not applicable
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from MCL cells using the TRIZOL Reagent (ThermoFisher) and validated for integrity and purity using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
 
Hybridization protocol 1.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent Hi-RPMI hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then scan immediately.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Dynamic Range of Green PMT is set to 100% and 10%).
Description Constitutive Gene expression of EOC cells.
Data processing The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1-v107_Sep09 and Grid: 014850_D_F_20100430) to obtain background subtracted and spatially detrended Processed Signal intensities.
 
Submission date Jan 18, 2017
Last update date Jul 24, 2017
Contact name Riccardo Bomben
E-mail(s) rbomben@cro.it
Phone +39 0434 659718
Organization name CRO Aviano
Department D-RT
Lab Clinical and Experimental Onco Hematology Unit
Street address Via Franco Gallini 2
City Aviano
ZIP/Postal code 33080
Country Italy
 
Platform ID GPL17077
Series (2)
GSE93793 Characterization of three Epithelial Ovarian Cancer cell lines resistant to cisplatin (mRNA).
GSE93795 Characterization of three Epithelial Ovarian Cancer cell lines resistant to cisplatin.

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
GE_BrightCorner 0.08887768
DarkCorner 0.13275194
A_23_P117082 -0.2186861
A_33_P3246448 -0.754539
A_33_P3318220 -0.1395719
A_33_P3236322 -0.17909455
A_33_P3319925 -0.4529624
A_21_P0000509 0.009606361
A_21_P0000744 0.504796
A_24_P215804 0.537539
A_23_P110167 0.37590218
A_33_P3211513 0.24863386
A_23_P103349 0.26221657
A_32_P61480 3.6231232
A_33_P3788124 -0.51526904
A_33_P3414202 1.170968
A_33_P3316686 0.31919813
A_33_P3300975 -0.31503582
A_33_P3263061 -0.12471104
A_33_P3261373 0.849787

Total number of rows: 50739

Table truncated, full table size 1231 Kbytes.




Supplementary file Size Download File type/resource
GSM2462177_US45102827_253949416318_S01_GE1_1105_Oct12_2_3_MDAH_miRES1.txt.gz 12.5 Mb (ftp)(http) TXT
Processed data included within Sample table

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