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Sample GSM3581874 Query DataSets for GSM3581874
Status Public on Jan 29, 2019
Title p53-/-_no-dox_0h
Sample type RNA
Source name HCT116 p53−/−, control, 0 h.
Organism Homo sapiens
Characteristics cell line: HCT116
genotype: p53−/−
treatment: no
time to harvest: 0 hour
Treatment protocol HCT116 p53+/+ and HCT116 p53−/− cells were treated with 2 μg/mL of doxorubicin for 2 hours. The cultures were incubated for 0, 12, 24, or 48 hours at 37 ºC in a humidified incubator with 5% CO2.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from the cells using RNeasy Plus Universal Mini Kits (Qiagen) according to the manufacturer’s instructions.
Label Cy3
Label protocol The fluorescent cRNA using cyanine 3-labelled (Cy3) targets was generated following the Agilent’s One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp labeling) protocol. The Cy3-labeled cRNA was purified by Rneasy Mini Kit (Qiagen) and quantified by Nanodrop-2000 Spectrophotometer.
Hybridization protocol Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction containing Agilent Fragmentation Buffer and Gene Expression Blocking Agent following the manufacturers instructions. Hi-RPM Hybridization Buffer was added to stop the fragmentation. Samples were hybridized to SurePrint G3 Human Gene Expression 8x60K Microarrays for 17 hours at 65°C with rotation. After hybridization, microarrays were washed 1 minute at room temperature with Gene Expression Wash Buffer 1 and 1 minute with 37°C pre-warmed Gene Expression Wash Buffer 2.
Scan protocol Slides were scanned on the Agilent Microarray Scanner using one color scan setting for 8x60K array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).
Description Gene expression in non-treated p53-null cells
Data processing The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028004_D_F_20140813) to obtain background subtracted and spatially detrended Processed Signal intensities.
Submission date Jan 28, 2019
Last update date Jan 29, 2019
Contact name Koichi Matsuda
Organization name The University of Tokyo
Street address 4-6-1, Shirokanedai, Minato-ku
City Tokyo
ZIP/Postal code 108-8639
Country Japan
Platform ID GPL13607
Series (1)
GSE125787 Identification of p53-regulated genes in wild-type p53 or p53-null HCT116 cells

Data table header descriptions
VALUE Normalized signal intensity

Data table
1 202656.6
2 2.778781
3 2.529906
4 463.5913
5 2530.063
6 102.0971
7 8757.7
8 6765.315
9 5.628648
10 32.43333
11 4.559861
12 1780.157
13 740.6471
14 2872.353
15 30247.96
16 2.724708
17 370.3804
18 145.1808
19 2.73906
20 1606.746

Total number of rows: 62976

Table truncated, full table size 904 Kbytes.

Supplementary file Size Download File type/resource
GSM3581874_US84403582_252800419147_S01_GE1_107_Sep09_1_1.txt.gz 3.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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