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Sample GSM1404603 Query DataSets for GSM1404603
Status Public on Sep 30, 2015
Title DLD1 FR10
Sample type RNA
Source name DLD1 cells with 10ng/ml of FR
Organism Homo sapiens
Characteristics cell type: colon cancer cells
cell line: DLD1
Treatment protocol Colon cancer cells were seeded at a density of one million cells in P10 plate. The next day, medium was changed to fresh medium with or without 10 ng/ml of FR901464. The cells were incubated for 24 hours at 37 ºC in a humidified incubator with 5% CO2.
Growth protocol Colon cancer cell lines were cultured in DMEM supplemented with 10% heat-inactivated fetal bovine serum.
Extracted molecule total RNA
Extraction protocol RNA was extracted using TRIzol and TRIzol RNA Purification kit (Invitrogen) following the manufacture's instructions.
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.
Hybridization protocol 0.6 ug of Cy3-labelled 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 manufacturer's instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K v2 Microarrays 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 immediately.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60K array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).
Description Gene expression with drug treatment
Data processing The scanned images were analyzed with Feature Extraction Software 10.10 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
Submission date Jun 05, 2014
Last update date Apr 23, 2018
Contact name Tomoki Yamano
Phone 81-798-45-6371
Organization name Hyogo College of Medicine
Department Department of Surgery
Lab Lower Gastrointestinal Surgery
Street address 1-1 Mukogawa-cho
City Nishinomiya
State/province Hyogo
ZIP/Postal code 663-8501
Country Japan
Platform ID GPL16699
Series (1)
GSE58241 Gene expression influenced by SF3B1 inhibitor, FR901464 or SF3B1 gene mutations in colorectal cancer cells
Reanalyzed by GSE113533

Data table header descriptions
VALUE Scaled signal intensity that adjust the average intensity value to 2500.

Data table
4 9109.450052
5 78.521702
6 13.32861192
7 105.4777147
8 66.55211798
9 6506.230481
10 336.2456362
11 52.30951487
12 6134.811888
13 2834.065713
14 333.2965875
15 13.70667498
16 13.72551578
17 239.7530145
18 219.475062
19 71.70094597
20 10286.81865
21 54.58662643
22 3968.154524
23 13.75737141

Total number of rows: 58717

Table truncated, full table size 1015 Kbytes.

Supplementary file Size Download File type/resource
GSM1404603_AR1272_06.txt.gz 3.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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