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Series GSE47637 Query DataSets for GSE47637
Status Public on Jun 05, 2013
Title Genome-wide DNA methylation profiling of KYSE180 cells transfected with HOTAIR vector using Illumina HumanMethylation 450 arrays
Organism Homo sapiens
Experiment type Methylation profiling by array
Summary To analysis of the effect of HOTAIR on global DNA methylation in KYSE180 esophageal cancer cell line, genome-scale DNA methylation was analyzed in a pair of esophageal cancer cell lines, KYSE180 cells stably transfected with HOTAIR and control KYSE180 cells. The results from genome-wide DNA methylation analysis indicate that hypermethylation occurs more frequently than hypomethylation after stably ectopic expressing HOTAIR in KYSE180 cells.
Overall design DNA was quantified by Quant-iT PicoGreen dsDNA Reagent (Invitrogen) and the integrity was analyzed in a 1.3% agarose gel. Bisulfite conversion of 600 ng of each sample was perform according to the manufacture's recommendation for Illumina Infinium Assay. Effective bisulphite conversion was checked for three controls that were converted simultaneously with the samples. 4 ul of bisulfite converted DNA were used to hybridize on Infinium HumanMethylation 450 BeadChip, following Illumina Infinium HD Methylation protocol. Chip analysis was performed using Illumina HiScan SQ fluorescent scanner. The intensities of the images are extracted using GenomeStudio (2010.3) Methylation module (1.8.5) software. Methylation score of each CpG is represented as beta value. For pairwise differential methylation analysis, the difference of two biological replicates of the ESCC cell lines KYSE180 and KYSE180_HOTAIR was calculated.
Contributor(s) Li X, Han W
Citation(s) 24022190
Submission date Jun 04, 2013
Last update date Mar 22, 2019
Contact name Weidong Han
Organization name Chinese PLA General Hospital
Department School of Life Sciences
Lab Department of Molecular Biology
Street address #28 Fuxing Road, HaiDian District
City Beijing
ZIP/Postal code 100853
Country China
Platforms (1)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (2)
GSM1153918 genomic DNA from KYSE180 cells transfected with control vector
GSM1153919 genomic DNA from KYSE180 cells transfected with HOTAIR vector
This SubSeries is part of SuperSeries:
GSE47639 KYSE180 cells transfected with HOTAIR compared to control cells
BioProject PRJNA207000

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE47637_RAW.tar 183.1 Mb (http)(custom) TAR
GSE47637_signal_intensities.txt.gz 6.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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