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Sample GSM3019012 Query DataSets for GSM3019012
Status Public on Feb 20, 2020
Title TP53-KO-ASTROCYTE-rep1
Sample type RNA
 
Source name TP53-KO-ASTROCYTE
Organism Mus musculus
Characteristics strain background: C57BL/6J
genotype/variation: TP53 knocked-out mice
tissue: brain
cell type: Astrocyte cells
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using TRIzol (Life Technologies) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-2000.
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technologies) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop 2000 Spectrophotometer.
 
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 SurePrint G3 Mouse GE 8×60K array slides (G4858A, Agilent Technologies) at 65 °C with rotation at 10 rpm for 17 hours in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 minute with 37°C GE Wash buffer 2 (Agilent Technologies), then dried immediately by brief centrifugation.
Scan protocol Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2565BA, Agilent Technologies) using one color scan setting for 8x60k array slides.
Description TP53-KO-ASTROCYTE#1
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_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
 
Submission date Feb 21, 2018
Last update date Feb 22, 2020
Contact name Keisuke Katsushima
E-mail(s) kkeisuke@med.nagoya-cu.ac.jp
Phone +81-052-853-8196
Organization name Nagoya City University Graduate School of Medical Sciences
Department Department of Epigenomics
Lab Yutaka Kondo
Street address 1 Kawasumi, Mizuho-cho, Mizuho-ku
City Nagoya
ZIP/Postal code 467-8601
Country Japan
 
Platform ID GPL10787
Series (2)
GSE110927 Expression analysis of MADM based glioma mouse model and normal brain
GSE110937 ChIP and expression analysis of MADM based glioma mouse model

Data table header descriptions
ID_REF
VALUE Normalized Log2 signal intensity

Data table
ID_REF VALUE
GE_BrightCorner 12.457807
DarkCorner 2.1207223
A_55_P2051983 2.0629683
A_52_P169082 5.5922513
A_30_P01028193 2.0589306
A_52_P237997 2.9377468
A_51_P414243 11.539526
A_55_P2136348 2.0526223
A_51_P108228 1.8871001
A_30_P01033363 4.8268766
A_55_P2049737 2.0455887
A_30_P01024440 8.226432
A_30_P01025554 11.622256
A_30_P01031558 4.4346485
A_30_P01030675 2.0355685
A_51_P328014 10.834343
A_30_P01019108 6.790096
A_55_P2056220 10.355884
A_55_P1985764 13.829121
A_52_P108321 6.9588776

Total number of rows: 55821

Table truncated, full table size 1289 Kbytes.




Supplementary file Size Download File type/resource
GSM3019012_TP53-KO-ASTROCYTE-rep1.txt.gz 11.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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