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Sample GSM1646206 Query DataSets for GSM1646206
Status Public on May 15, 2021
Title PNT1A_DHS_1e-8M_rep4
Sample type RNA
 
Source name PNT1A_48hr_1e-8M DHS
Organism Homo sapiens
Characteristics tissue origin: prostate
Stage: non cancerous
cell line: PNT1A
cell type: prostate cell line
treated with: 1e-8M DHS for 48hrs
Treatment protocol PNT1A cells were treated with 1e-06 M (mid) or 1e-08 M (low) of plasticizers, or 0.4% DMSO (vehicle) for 48h at 37°C and 5% CO2
Growth protocol PNT1A cells were grown at 37°C, 5% CO2 in RPMI 1640 supplemented with 0.025 M glucose, 2mM glutamine, 10mM Hepes, 1mM sodium pyruvate and 0.018 M sodium bicarbonate, 10% head inactivated fetal bovine serum (FBS), 100 IU/mL of penicillin and 100 ug/mL of streptomycin
Extracted molecule total RNA
Extraction protocol RNA was prepared using the RNEasy Plus Mini Kit, according to the manufacturer's protocol. RNA quality and quantification was obtained using the Bioanalyzer 2000 and the Nano 6000 RNA kit. Protein and other contaminants were assessed using the NanoDrop 2000.
Label Cy3
Label protocol 25 ng of total RNA was used for labeling, according to Agilent's One color Low Input Quick Amp labeling kit protocol.
 
Hybridization protocol 600 ng of Cy3-labelled cRNA (specific activity >10.0 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 manufacturers 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 GE 8x60K microarrays (G4851A) 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), dried briefly and put in Agilent Ozone-Barrier Slide holder.
Scan protocol Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides
Description Gene expression after 48hr incubation with DHS 1e-8M
DHS_low_4
Data processing The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid 028004_D_F_20120411) to obtain background subtracted and Processed Signal intensities.
Please note that control probes were filtered out and only probes for which there was at least 4 samples with normalized signal of at least 10% higher to the background were included in the analysis.
 
Submission date Mar 29, 2015
Last update date May 15, 2021
Contact name Claudia Lalancette
E-mail(s) clalance@umich.edu
Organization name McGill University
Department Pharmacology and Therapeutics
Street address 3655 Sir William Osler
City Montreal
State/province QC
ZIP/Postal code H3Y 1G6
Country Canada
 
Platform ID GPL14550
Series (2)
GSE67396 A Hightroughput Approach for Screening Potential Green Plasticizers Using A Human Prostate Cell Line [set1]
GSE67399 A Hightroughput Approach for Screening Potential Green Plasticizers Using A Human Prostate Cell Line

Data table header descriptions
ID_REF
VALUE quantile normalized

Data table
ID_REF VALUE
A_23_P326296 7.878405321
A_24_P287941 9.433016761
A_24_P325046 5.140609232
A_23_P200404 10.89814758
A_19_P00800513 10.1651567
A_23_P15619 9.728563708
A_33_P3402354 6.010022642
A_32_P98683 8.555287202
A_23_P137543 9.390531174
A_19_P00803040 9.253785779
A_23_P117852 13.70104568
A_24_P328231 6.513452486
A_24_P186124 10.73283235
A_23_P369983 9.69563027
A_23_P325676 6.952706352
A_24_P37441 8.558064127
A_23_P20980 12.44935299
A_23_P123265 9.852309238
A_23_P339687 11.2592467
A_23_P25030 6.674707205

Total number of rows: 29007

Table truncated, full table size 718 Kbytes.




Supplementary file Size Download File type/resource
GSM1646206_SG11514161_252800420076_S001_GE1_1105_Oct12_1_3.txt.gz 3.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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