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Sample GSM3488736 Query DataSets for GSM3488736
Status Public on Jan 28, 2019
Title HCT116_ARID1A-KO_APR-246_0hr_rep2
Sample type RNA
Source name HCT116, ARID1A-KO, APR-246, 0hr, replicate2
Organism Homo sapiens
Characteristics cell line: HCT116
genotype: ARID1A-KO
Treatment protocol ARI1DA-WT and ARID1A-KO HCT116 cancer cells were treated with 0 or 40 μM APR-246. After 24 h, total RNA was extracted.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the Qiagen RNeasy kit.
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.25 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
Hybridization protocol cDNA was hybridized to Agilent microarrays (SurePrint G3 Human Gene Expression 8 x 60K Ver.1.0, G4851: 42405 probes) using a Gene Expression Hybridization Kit (Agilent Technologies) for 16 h at 65°C in duplicate.
Scan protocol After the arrays were washed using the Gene Expression Wash Pack (Agilent Technologies), the data were extracted using an Agilent scanner.
Description Gene expression after 24hr in 0 μM APR-246 treated cells
Data processing The arrays were first analyzed using the Feature Extraction software (Agilent Technologies).
Submission date Nov 26, 2018
Last update date Jan 28, 2019
Contact name Takashi Kohno
Phone +81-3-3547-2511 (4650)
Organization name National Cancer Center Research Institute
Lab Division of Genome Biology
Street address 1-1, Tsukiji 5-chome
City Chuo-ku
State/province Tokyo
ZIP/Postal code 104-0045
Country Japan
Platform ID GPL13607
Series (1)
GSE122925 Genome-wide gene expression analysis in treatment for 24 h with 40 μM APR-246 in ARID1A-WT and ARID1A-KO HCT116 cells.

Data table header descriptions
VALUE Normalized signal intensity

Data table
1 3294.801
2 2.854337
3 2.872492
4 16.36662
5 70.69141
6 10.69932
7 182.8771
8 220.3116
9 4.311847
10 4.107588
11 2.979152
12 97.25734
13 11.8106
14 74.70789
15 1537.747
16 8.401512
17 13.74006
18 3.230786
19 3.018221
20 119.5756

Total number of rows: 62976

Table truncated, full table size 904 Kbytes.

Supplementary file Size Download File type/resource
GSM3488736_US85000263_252800421788_S01_GE1_107_Sep09_2_3.txt.gz 3.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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