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Sample GSM2292539 Query DataSets for GSM2292539
Status Public on Feb 24, 2017
Title Control, rep. 2 [re-analysis]
Sample type RNA
 
Source name Control A-498 cells
Organism Homo sapiens
Characteristics cell line: A-498 (ATCC HTB-44)
tumor type: renal cell carcinoma
gender: female
treated with: CONTROL vehicle for 3hrs
Treatment protocol A498 cells were plated in complete RPMI onto 100 mm dishes at 0.9 x 10E6 cells per dish. After cells were allowed to adhere overnight, cells were refed with complete RPMI containing 0.1% DMSO (vehicle) for 3 hours or 100 nM englerin A for 8 hours.
Growth protocol A498 cells were purchased from ATTC and maintained in RPMI medium supplemented with 10% FBS, 2 mM L-glutamine, and 100 units/ml penicillin/streptomycin (complete RPMI). All experiments were conducted with cells of passage number less than 25.
Extracted molecule total RNA
Extraction protocol Cell extracts were prepared using 1 ml of TRI Reagent (Zymo Research, Irvine, CA) per dish. Total RNA was then purified from cell extracts using spin columns by Zymo Research according to the manufacturer’s directions.
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng total RNA using the 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 a NanoDrop 2000c Spectrophotometer.
 
Hybridization protocol 600 ng of Cy3-labelled cRNA (specific activity >= 15.6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human Gene Expression 8x60K v2 Microarrays (G4851B-039494) 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 immersed in acetonitrile and dried immediately by slowly removing the slide.
Scan protocol Slides were scanned immediately after washing on an Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green at 20 bit).
Description US10130359_253949437667_S01_GE1_107_Sep09_2_2.txt
Data processing The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid 039494_D_F_20140813) to obtain background subtracted and spatially detrended Processed Signal intensities. Data was uploaded into Genespring version 11.5.1 where was thresholded to 1.0, log2 transformed, quantile normalized and base line transformed using the median of all samples. Data was filtered by flags in a way that at least 75% of the samples in any of the 2 experimental groups had DETECTED flags. Then, differentially expressed genes were determined using a moderated t-test statistics with p-value 0.01 and fold change 1.5 as cutoffs.
 
Submission date Aug 25, 2016
Last update date Feb 24, 2017
Contact name Diego Altomare
Organization name University of South Carolina
Department Department of Drug Discovery and Biomedical Sciences
Lab Functional Genomics Core
Street address 715 Sumter Street, Room 617
City Columbia
State/province SC
ZIP/Postal code 29208
Country USA
 
Platform ID GPL17077
Series (2)
GSE86045 Gene expression analysis of renal cell carcinoma cell line A-498 after 8-hour treatment with englerin A.
GSE86047 Gene Expresion Analysis of A-498 cells after treatment with Englerin A
Relations
Reanalysis of GSM2292531

Data table header descriptions
ID_REF
VALUE Normalized signal intensity (Background corrected, thresholded to 1.0, log2 transformed, quantile normalized and base line transformed using the median of all samples).

Data table
ID_REF VALUE
GE_BrightCorner 0.24161911
DarkCorner 0.032690287
A_23_P117082 0.08749008
A_33_P3246448 -0.47062492
A_33_P3318220 0.80472326
A_33_P3236322 1.4127841
A_33_P3319925 0.021355629
A_21_P0000509 -0.115501404
A_21_P0000744 0.3375597
A_24_P215804 0.2769699
A_23_P110167 0.031867027
A_33_P3211513 -0.6790428
A_23_P103349 0.070430994
A_32_P61480 1.1052325
A_33_P3788124 0.023473024
A_33_P3414202 -0.28988838
A_33_P3316686 -0.15415764
A_33_P3300975 0.5070772
A_33_P3263061 0.060465813
A_33_P3261373 -0.15271568

Total number of rows: 50739

Table truncated, full table size 1238 Kbytes.




Supplementary file Size Download File type/resource
GSM2292539_US10130359_253949437667_S01_GE1_107_Sep09_2_2.txt.gz 3.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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