Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Methylation profiling of human first and thrid trimester placenta and whole blood

ABSTRACT: Fifteen DNA methylation array experiments were performed on five human chromosome specific array platforms (NimbleGen: HG18_CHR13_FT, HG18_CHR18_FT, HG18_CHR21_FT, HG18_CHRX_FT, HG18_CHRY_FT), comparing: (1) one female whole blood immunoprecipitated DNA fragments to their input DNA, (2) one 1st trimester normal placenta immunoprecipitated DNA fragments to their input DNA and (3) one 3rd trimester normal placenta immunoprecipitated DNA fragments to their input DNA.

ORGANISM(S): Homo sapiens

SUBMITTER: Stephen Clayton

PROVIDER: E-TABM-507 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Publications

Sites of differential DNA methylation between placenta and peripheral blood: molecular markers for noninvasive prenatal diagnosis of aneuploidies.

Papageorgiou Elisavet A EA Fiegler Heike H Rakyan Vardhman V Beck Stephan S Hulten Maj M Lamnissou Klea K Carter Nigel P NP Patsalis Philippos C PC

The American journal of pathology 20090406 5

The use of epigenetic differences between maternal whole blood and fetal (placental) DNA is one of the main areas of interest for the development of noninvasive prenatal diagnosis of aneuploidies. However, the lack of detailed chromosome-wide identification of differentially methylated sites has limited the application of this approach. In this study, we describe an analysis of chromosome-wide methylation status using methylation DNA immunoprecipitation coupled with high-resolution tiling oligon ...[more]

PMID: 19349366

Similar Datasets

Project description:To understand downstream genes affected by overexpression of OsbHLH148, the Rice 3’-Tiling Microarray analysis (GreenGene Biotech, Yongin, Korea) was carried out to profile gene expression of OsCc1:OsbHLH148 transgenic plants in comparison with wild-type plants under normal growth conditions. RNA samples from these plants were used to generate cyanine-3 (Cy3)-labeled complementary DNA (cDNA) probes, which were then hybridized to the microarray. Each data set was obtained from two biological repeats with independent transgenic lines. Expression profiling was conducted using a Rice 3’-Tiling Microarray. Information on the microarray can be found at http://www.ggbio.com (GreenGene Biotech). The Rice 3’-Tiling Microarray was designed from 27,448 genes deposited at IRGSP, RAP1 database (http://rapdb.lab.nig.ac.jp). Among these, 20,507 genes were from representative RAP1 sequences with cDNA/EST supports and 6,941 genes were predicted without cDNA/EST supports. Ten 60-nt long probes were designed from each gene starting 60 bp ahead the end of stop codon with 10 bp shifts in position so that 10 probes covered 150 bp in the 3' region of the gene. In total, 270,000 probes were designed (average size, 60-nt) to have Tm values of 75 to 85 °C. The microarray was manufactured by NimbleGen Inc. (http://www.nimblegen.com/). Random GC probes (38,000) were used to monitor the hybridization efficiency and fiducial markers at the four corners (225) were included to assist with overlaying the grid on the image. The microarray was used to profile gene expression in OsCc1:OsbHLH148 transgenic and wild-type rice plants. Cy3-labeled target cDNA fragments were synthesized from two-week old seedlings using a Cy3-9mer primer. For normalization, data were processed with cubic alpine normalization using quartiles to adjust signal variation between chips and with Rubust Multi-Chip Analysis using a median polish algorithm implemented in NimbleScan (Workman et al., 2002; Irizarry et al., 2003). To assess the reproducibility of the microarray analysis, we repeated the experiment two times with independent transgenic lines, T-2 and T-9, and analyzed each data set statistically using one-way ANOVA.

Project description:To identify genes that are regulated by MeJA and drought, global expression profilings were performed on panicles from Ubi1:AtJMT, drought-treated NT, and untreated NT plants. The underlying assumption of this approach was that high levels of MeJA produced either by overexpression of AtJMT in the transgenic panicles or by drought treatment in the NT panicles regulates genes that are involved in spikelet and/or panicle development. Profiling was conducted using the Rice 3M-bM-^@M-^Y-Tiling Microarray (GreenGene Biotech, Yongin, Korea). RNA samples from S1 panicles of Ubi1:AtJMT, drought-treated NT and untreated NT plants were used to generate cyanine-3 (Cy3)-labeled complementary DNA (cDNA) probes, which were then hybridized to the microarray. Each data set was obtained from three biological repeats. Expression profiling was conducted using a Rice 3M-bM-^@M-^Y-Tiling Microarray. Information on the microarray can be found at http://www.ggbio.com (GreenGene Biotech). The Rice 3M-bM-^@M-^Y-Tiling Microarray was designed from 27,448 genes deposited at IRGSP, RAP1 database (http://rapdb.lab.nig.ac.jp). Among these, 20,507 genes were from representative RAP1 sequences with cDNA/EST supports and 6,941 genes were predicted without cDNA/EST supports. Ten 60-nt long probes were designed from each gene starting 60 bp ahead the end of stop codon with 10 bp shifts in position so that 10 probes covered 150 bp in the 3' region of the gene. In total, 270,000 probes were designed (average size, 60-nt) to have Tm values of 75 to 85 M-BM-0C. The microarray was manufactured by NimbleGen Inc. (http://www.nimblegen.com/). Random GC probes (38,000) were used to monitor the hybridization efficiency and fiducial markers at the four corners (225) were included to assist with overlaying the grid on the image. The microarray was used to profile gene expression in Ubi1:AtJMT, drought-treated NT, and untreated NT plants. Cy3-labeled target cDNA fragments were synthesized from S1 panicles using a Cy3-9mer primer. For normalization, data were processed with cubic alpine normalization using quartiles to adjust signal variation between chips and with Rubust Multi-Chip Analysis using a median polish algorithm implemented in NimbleScan (Workman et al., 2002; Irizarry et al., 2003). To assess the reproducibility of the microarray analysis, we repeated the experiment three times with independently prepared total RNAs.

Dataset Information

Methylation profiling of human first and thrid trimester placenta and whole blood

Publications

Sites of differential DNA methylation between placenta and peripheral blood: molecular markers for noninvasive prenatal diagnosis of aneuploidies.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure