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Sample GSM2460779 Query DataSets for GSM2460779
Status Public on Jan 18, 2017
Title chitosan
Sample type RNA
Source name Cell cultured on Chitosan membrane
Organism Homo sapiens
Characteristics cell line: HT29
cell type: colon cancer cell line
Extracted molecule total RNA
Extraction protocol RNA was prepared using the RNeasy Mini Purification kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy Mini column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
Hybridization protocol 1.5 ug 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 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) 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 by brief centrifugation.
Scan protocol Slides were scanned immediately after washing on the Agilent High-Resolution Microarray Scanner using one color scan setting for 8x60kv2 array slides.
Data processing The scanned images were analyzed with R using limma package.
Submission date Jan 17, 2017
Last update date Apr 23, 2018
Contact name Keisuke Sekine
Organization name National Cancer Center Research Institute, Japan
Department Graduate School of Medicine
Lab Laboratory of Cancer Cell Systems
Street address 5-1-1 Tsukiji
City Chuo-ku
State/province Tokyo
ZIP/Postal code 104-0045
Country Japan
Platform ID GPL16699
Series (1)
GSE93704 Chitosan promotes cancer progression and stem cell properties through Wnt signaling in colon and hepatocellular carcinoma cells
Reanalyzed by GSE113533

Data table header descriptions
VALUE The raw signal intensities of samples were log2-transformed and normalised by the quantile algorithm.

Data table
1 -0.201421865
2 -0.270634534
3 -0.122967799
4 0.121862595
5 -0.252066679
6 -0.435737192
7 0.036265599
8 -0.330413435
9 -0.097544608
10 0.28233845
11 0.182751595
12 0.326504819
13 0.146860065
14 -0.188962253
15 -0.186815939
16 -0.357806233
17 0.10641012
18 0.0795972
19 -0.016940081
20 0.122514597

Total number of rows: 62976

Table truncated, full table size 1135 Kbytes.

Supplementary file Size Download File type/resource
GSM2460779_US3.txt.gz 3.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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