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Sample GSM712014 Query DataSets for GSM712014
Status Public on Apr 01, 2017
Title PC3GLI1ER_0hrs (control)
Sample type RNA
 
Source name PC3GLI1ER, 0hrs
Organism Homo sapiens
Characteristics cell line: PC3GLI1ER (derived from prostate cancer cell line PC3)
agent: control
time: 0 hrs
Treatment protocol 10 nM of beta-estradiol (E2) was added to the medium.
Growth protocol Cells were maintained in DMEM containing 10% of activated-charcoal treated FBS.
Extracted molecule total RNA
Extraction protocol QIAGEN RNeasy mini kit was used.
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
 
Hybridization protocol 1.65 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x GEx Hybridization buffer HI-RPM (Agilent) was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays 4x44k (G4112F) 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 rinsed with Acetonitrile for cleaning up and drying.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides.
Description PC3GLI1ER control
Data processing The scanned images were analyzed with Feature Extraction Software 9.1.3.1 (Agilent) using default parameters (protocol GE1-v5_91_0806 and Grid: 014850_D_20060725) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
 
Submission date Apr 20, 2011
Last update date Apr 01, 2017
Contact name Shingo Inaguma
Organization name Aichi Medical University School of Medicine
Department Department of Pathology and Promoting Center for Clinical Research
Street address Nagakute
City Aichi
ZIP/Postal code 480-1195
Country Japan
 
Platform ID GPL6480
Series (2)
GSE28899 Identification of GLI1 direct target genes in human prostate cancer cell line PC3
GSE28900 Identification of GLI1 direct and indirect target genes in human prostate cancer cell line PC3

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
DarkCorner 0.061
A_24_P66027 26.546
A_32_P77178 0.076
A_23_P212522 5.241
A_24_P934473 0.263
A_24_P9671 135.239
A_32_P29551 0.098
A_24_P801451 3.559
A_32_P30710 193.262
A_32_P89523 0.320
A_24_P704878 0.075
A_32_P86028 532.325
A_24_P470079 0.098
A_23_P65830 19.540
A_23_P109143 67.468
A_24_P595567 0.074
A_24_P391591 1.726
A_24_P799245 0.073
A_24_P932757 0.073
A_24_P835500 118.092

Total number of rows: 41062

Table truncated, full table size 761 Kbytes.




Supplementary file Size Download File type/resource
GSM712014_US12302318_251485011806_S01_GE1-v5_91_0806_1_1.txt.gz 5.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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