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Sample GSM1686189 Query DataSets for GSM1686189
Status Public on Dec 31, 2015
Title Primary prostate p53-/- Rb∆f/∆f 2
Sample type RNA
 
Source name Prostate, Cre
Organism Mus musculus
Characteristics tissue: prostate
genotype: p53-/- Rb deltaf/deltaf
rb status: Deleted
pten status: Intact
Treatment protocol Prostate cells were infected with adeno virus (lacZ) as a control or adeno virus (Cre) for deleting Rb overnight followed by changing of media. RNA was extracted after infection by 48 hours.
Growth protocol Prostate cells were cultured in FBS lack Prostacult media supplemented with bFGF and bEGF
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using RNeasy Mini Kit (#74106, Qiagen) according to the manufacturer’s instruction. RNA was quantified, and quality was monitored by the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions with some changes. 3rd Spike mix was made by diluted 2nd Spike-Mix 10 times, and 1.8 ul of 3rd Spike-Mix was added to samples. Cy3 labeled cRNA was synthesized at 40°C for 2 hours and purified by RNAeasy 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 >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse Whole Genome Microarray 4x44K v2 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 dried by raise it slowly from buffer 2.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green.
Description Gene expression of p53-/- prostate cells in the depletion of Rb
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: 026655_D_F_20120201) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Entities having Detected flag across all samples were extracted.
 
Submission date May 14, 2015
Last update date Dec 31, 2015
Contact name Takumi Nishiuchi
E-mail(s) tnish9@staff.kanazawa-u.ac.jp
Organization name Kanazawa University
Street address 13-1 Takaramachi
City Kanazawa
ZIP/Postal code 920-0934
Country Japan
 
Platform ID GPL11202
Series (2)
GSE68903 Development of gene sets after deleting Rb in p53 null background primary prostate cells [Rb only]
GSE68905 Development of gene sets after deleting Rb or Rb and Pten in p53 null background primary prostate cells

Data table header descriptions
ID_REF
VALUE Normalized Signal intensity

Data table
ID_REF VALUE
GE_BrightCorner 3.5854225
A_55_P2022211 0.7783022
A_55_P1964375 1.5580587
A_51_P128876 6.012415
A_51_P207591 -2.522789
A_55_P2131920 3.1614304
A_55_P2404223 -2.1706715
A_55_P2101944 0.7567768
A_52_P358860 0.10827446
A_51_P119031 -0.53681755
A_51_P343900 3.2136126
A_51_P487813 3.361517
A_52_P613977 1.6780977
A_52_P549166 0.4637127
A_55_P2052210 4.6008472
A_51_P128987 4.840103
A_55_P1958431 -5.1533737
A_55_P2111153 1.3288012
A_51_P210560 2.449132
A_55_P2048493 -3.1282568

Total number of rows: 22177

Table truncated, full table size 520 Kbytes.




Supplementary file Size Download File type/resource
GSM1686189_SG12060621_252665516621_S01_GE1_1100_Jul11_1_1.txt.gz 2.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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