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Sample GSM729620 Query DataSets for GSM729620
Status Public on May 25, 2011
Title PPARG_BMP2_2of2
Sample type genomic
 
Channel 1
Source name ppar-gamma ChIP DNA from BMP2 treated HPAEC
Organism Homo sapiens
Characteristics cell type: human pulmonary artery endothelial cells
chip antibody: ppar-gamma
Treatment protocol Cells were treated with recombinant human BMP2 (Sigma-Aldrich) for 4 hours before harvesting.
Growth protocol HPAECs from large vessels (ScienCell) were grown in commercial EC media supplied by ScienCell (Cat: 1001) and used at passages 4-8.
Extracted molecule genomic DNA
Extraction protocol ChIP was performed on 10x10^6 HPAECs with anti-ppar-gamma (Santa Cruz; sc-7273X) and anti-beta-catenin (UPSTATE; Cat 06-734) antibodies using the Farnham ChIP protocol. The immunoprecipitated DNA was amplified using the Whole Genome Amplification Kit (Sigma).
Label Cy5
Label protocol Input DNA was labeled with Cy3 and ChIP DNA was labeled with Cy5 using the Standard NimbleGen ChIP labeling protocol (1 ug of amplified ChIP DNA, direct incorporation of Cy-labeled primers with Klenow extension).
 
Channel 2
Source name Input DNA from BMP2 treated HPAEC
Organism Homo sapiens
Characteristics cell type: human pulmonary artery endothelial cells
chip antibody: none, input DNA
Treatment protocol Cells were treated with recombinant human BMP2 (Sigma-Aldrich) for 4 hours before harvesting.
Growth protocol HPAECs from large vessels (ScienCell) were grown in commercial EC media supplied by ScienCell (Cat: 1001) and used at passages 4-8.
Extracted molecule genomic DNA
Extraction protocol ChIP was performed on 10x10^6 HPAECs with anti-ppar-gamma (Santa Cruz; sc-7273X) and anti-beta-catenin (UPSTATE; Cat 06-734) antibodies using the Farnham ChIP protocol. The immunoprecipitated DNA was amplified using the Whole Genome Amplification Kit (Sigma).
Label Cy3
Label protocol Input DNA was labeled with Cy3 and ChIP DNA was labeled with Cy5 using the Standard NimbleGen ChIP labeling protocol (1 ug of amplified ChIP DNA, direct incorporation of Cy-labeled primers with Klenow extension).
 
 
Hybridization protocol Standard NimbleGen hybridization kits and protocols were used and hybridization was performed using a NimbleGen 12 slide hybridization system.
Scan protocol Arrays were scanned with Axon scanner at 5 um resolution according to standard NimbleGen protocols.
Description HPAEC ChIP-chip anti-ppar-gamma BMP2 treated 2of2
Data processing Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.5 ChIP data extraction. Log2 ChIP/input ratios were created from the two raw pair files.
 
Submission date May 23, 2011
Last update date May 25, 2011
Contact name Molong Li
E-mail(s) molong.li@jhmi.edu
Organization name Johns Hopkins University
Department School of Medicine
Street address 733 N. Broadway
City Baltimore
State/province MD
ZIP/Postal code 21205
Country USA
 
Platform ID GPL6326
Series (1)
GSE29489 ChIP-chip of BMP2 or control treated human pulmonary artery endothelial cells with anti-beta-catenin or anti-ppar-gamma antibodies on promoter regions

Data table header descriptions
ID_REF
VALUE scaled, log2 (ChIP/Input) ratio

Data table
ID_REF VALUE
CHR10P045122163 -0.83
CHR10P045122263 -0.36
CHR10P045122363 0.08
CHR10P045122463 0.17
CHR10P045122563 -0.02
CHR10P045122663 0.22
CHR10P045122763 -0.14
CHR10P045122863 -0.34
CHR10P045122963 -0.24
CHR10P045123063 -0.04
CHR10P045123163 0.51
CHR10P045123563 -0.73
CHR10P045123663 -0.79
CHR10P045123763 0.01
CHR10P045123963 0.31
CHR10P045124063 -0.48
CHR10P045124163 -0.48
CHR10P045124263 -0.02
CHR10P045124363 -0.48
CHR10P045124463 -0.14

Total number of rows: 378961

Table truncated, full table size 7877 Kbytes.




Supplementary file Size Download File type/resource
GSM729620_PPARG_BMP2_2of2_532.pair.gz 7.0 Mb (ftp)(http) PAIR
GSM729620_PPARG_BMP2_2of2_635.pair.gz 7.0 Mb (ftp)(http) PAIR
GSM729620_PPARG_BMP2_2of2_ratio.gff.gz 4.7 Mb (ftp)(http) GFF
Processed data included within Sample table
Processed data provided as supplementary file

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