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Sample GSM442663 Query DataSets for GSM442663
Status Public on May 31, 2011
Title Huh7 EZH2 ChIP-chip Replicate 1 Slide 2
Sample type genomic
 
Channel 1
Source name Huh7 cells immunoprecipitated
Organism Homo sapiens
Characteristics cell line: Huh7
Treatment protocol No treatment was performed. EZH2 target genes in normal condition were identified.
Growth protocol The 2 HCC cell lines were maintained in DMEM supplemented with 10% FBS.
Extracted molecule genomic DNA
Extraction protocol ChIP assays were performed as described previously (Lee et al. Nat Protoc 2006;1:729-748). IP and input DNA were then purified with standard phenol/chloroform method.
Label Cy5
Label protocol DNA were amino-allyl labelled using randomly-primed, Klenow-based extension protocol. Cy5/3 dye was then incorporated into the DNA using in-direct labeling by incubating the dye with DNA for 3 hours.
 
Channel 2
Source name Huh7 cells input
Organism Homo sapiens
Characteristics cell line: Huh7
Treatment protocol No treatment was performed. EZH2 target genes in normal condition were identified.
Growth protocol The 2 HCC cell lines were maintained in DMEM supplemented with 10% FBS.
Extracted molecule genomic DNA
Extraction protocol ChIP assays were performed as described previously (Lee et al. Nat Protoc 2006;1:729-748). IP and input DNA were then purified with standard phenol/chloroform method.
Label Cy3
Label protocol DNA were amino-allyl labelled using randomly-primed, Klenow-based extension protocol. Cy5/3 dye was then incorporated into the DNA using in-direct labeling by incubating the dye with DNA for 3 hours.
 
 
Hybridization protocol Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential
Scan protocol Scanned on an Agilent G2505B scanner.
Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).
Description Huh7 Replicate 1 of 2
Data processing Agilent Feature Extraction Software (10.5.1.1) was used for background subtraction and LOWESS normalization.
 
Submission date Aug 20, 2009
Last update date May 31, 2011
Contact name Richard KW CHOY
E-mail(s) richardchoy@cuhk.edu.hk
Phone 852-26323099
Fax 852-26360008
Organization name The Chinese University of Hong Kong
Department Obstetrics & Gynaecology
Street address 1/F, Block E, Prince of Wales Hospital
City Shatin
ZIP/Postal code SAR
Country Hong Kong
 
Platform ID GPL4125
Series (1)
GSE17733 Delineation of EZH2 oncogenic functions in hepatocellular carcinoma

Data table header descriptions
ID_REF
VALUE normalized log10 ratio test/reference

Data table
ID_REF VALUE
1 6.508568333e-003
2 0.000000000e+000
3 -8.516723478e-002
4 -9.820170254e-002
5 4.548896889e-002
6 -4.020136483e-001
7 4.318685429e-002
8 5.166853215e-002
9 -5.795763027e-002
10 -1.773548465e-001
11 3.984468667e-002
12 2.285123851e-002
13 7.515635555e-002
14 4.692264189e-002
15 -5.778493363e-002
16 -6.131678013e-002
17 -5.417033815e-002
18 -2.528268430e-002
19 -1.196910695e-001
20 -7.645978594e-002

Total number of rows: 243485

Table truncated, full table size 5705 Kbytes.




Supplementary file Size Download File type/resource
GSM442663_Huh7_1_2.txt.gz 69.1 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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