GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM3581880 Query DataSets for GSM3581880
Status Public on Jan 29, 2019
Title p53+/+_dox_24h
Sample type RNA
Source name HCT116 p53+/+, doxorubicin, 24 h.
Organism Homo sapiens
Characteristics cell line: HCT116
genotype: p53+/+
treatment: doxorubicin
time to harvest: 24 hours
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 after 24h in doxorubicin-treated wild-type p53 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 218870.9
2 3.739233
3 3.753696
4 417.9139
5 2772.612
6 30.42975
7 16668.42
8 8529.303
9 14.63563
10 12.50156
11 4.804619
12 564.9646
13 770.9828
14 2106.658
15 38292.35
16 3.830858
17 266.2963
18 99.71914
19 3.824353
20 1422.069

Total number of rows: 62976

Table truncated, full table size 904 Kbytes.

Supplementary file Size Download File type/resource
GSM3581880_US84403582_252800419147_S01_GE1_107_Sep09_2_3.txt.gz 3.1 Mb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap