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Sample GSM2220244 Query DataSets for GSM2220244
Status Public on Aug 16, 2016
Title hiPS_ECC4_rep1
Sample type RNA
Source name Cancer Stem Cell, induced from human iPS cell with culture medium of ECC4, replicate 1
Organism Homo sapiens
Characteristics cell type: Cancer Stem Cell, induced from human iPS cell with culture medium of ECC4
gender: Female
age: 36
Growth protocol Human iPS cells kept undifferentiated were cultured in induction medium to allow differentiation. During the induction of differentiation, half of the medium was exchanged every day and the cells were passaged once or twice every two weeks. The period of induction of differentiation was at least 28 days, and at most two months. The cells were cultured at 37 °C under the atmosphere of 2% CO2.
Extracted molecule total RNA
Extraction protocol Total RNA was prepared with the RNeasy column purification (QIAGEN) according to the manufacturer'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 0.6ug 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 SurePrint G3 Human GE 8x60K Microarray Ver2.0 (Agilent) 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).
Scan protocol Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) 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 of induced cancer stem cell established from human iPS cell with ECC4 cell culture medium
Data processing The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
Normalized signal intensity by Agilp in series supplementary file.
Submission date Jun 29, 2016
Last update date Apr 23, 2018
Contact name Akimasa Seno
Organization name Okayama University
Department Applied Chemistry and Biotechnology
Lab Nano-Biotechnology
Street address 1-1, Tsushima-Naka, 1-chome, Kita-Ku
City Okayama
State/province Okayama
ZIP/Postal code 7008530
Country Japan
Platform ID GPL17077
Series (2)
GSE83880 Gene expression of developed cancer stem cells [OCC-hiPS]
GSE83883 Gene expression of developed cancer stem cells
Reanalyzed by GSE113533

Supplementary file Size Download File type/resource
GSM2220244_OCC-hiPS-16.txt.gz 3.0 Mb (ftp)(http) TXT
Processed data are available on Series record

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