Project description:Genome wide DNA methylation analysis of 96 adult and 14 fetal liver samples The study includes 110 individuals, 14 fetal and 96 adult samples, no replicates. Liver samples from 14 fetuses were obtained at gestational week 8-12. Adult liver samples were collected from 52 organ donors who had met accidental death and 44 liver samples from patients undergoing liver resection due to malignant tumors, most commonly from patients with metastatic colon cancers. Liver biopsies from these patients were collected from 'healthy' tissue that showed no visible pathological changes compared to the adjacent tumor.
Project description:Genome wide expression analysis of 92 adult and 14 fetal liver samples The study includes 106 individuals, 14 fetal and 92 adult samples, no replicates. Liver samples from 14 fetuses were obtained at gestational week 8-12. Adult liver samples were collected from 50 organ donors who had met accidental death and 42 liver samples from patients undergoing liver resection due to malignant tumors, most commonly from patients with metastatic colon cancers. Liver biopsies from these patients were collected from 'healthy' tissue that showed no visible pathological changes compared to the adjacent tumor.
Project description:Determine methylation pattern in PDAC a genome-wide analysis was performed in a cohort of 167 PDAC and 29 adjacent pancreatic tissues samples using the Infinium 450k methylation arrays (Illumina). 167 pancreatic tumors (PDAC) x 29 adjacent -non tumor samples.
Project description:DNA hydroxymethylation is frequently lost in glioblastoma. We hypothesized that reduced 5hmC levels might be related to the impaired expression of TET proteins in brain tumors. In this study we performed a genome-wide methylation analysis of LN229 cells stably transfected with scramble or TET3 overexpressing vectors. TET3 overexpression partially restored the genome-wide patterns of 5hmC characteristic of control brain samples in glioblastoma cell lines.
Project description:Human pluripotent stem cells hold great potential for regenerative medicine, but existing cell types have imitations. Human embryonic stem cells derived from fertilized embryos (IVF-ESCs) are considered the “gold standard”, but are allogeneic to potential recipients. Autologous induced pluripotent stem cells (iPSCs) can be produced from somatic cells by forced expression of pluripotency-associated factors, but are prone to genetic and epigenetic aberrations. To determine whether accumulation of such aberrations is intrinsic to somatic cell reprogramming, or secondary to the reprogramming method, we employed an alternative approach by somatic cell nuclear transfer (SCNT). SCNT-based reprogramming to NT-ESCs is mediated by factors present in oocyte’s cytoplasm, thus mimicking early embryogenesis. We generated genetically matched pluripotent stem cells and conducted genome-wide genetic, epigenetic and transcriptional analyses. We discovered that unlike iPSCs, NT-ESCs have a low burden of de novo copy number variations (CNVs), reflecting superior maintenance of genetic stability. Moreover, DNA methylation and transcriptome profiles of NT-ESCs corresponded closely to those of IVF-ESCs. In contrast, iPSCs harbored methylation abnormalities including residual CpG methylation typical of parental fibroblasts, suggesting incomplete reprogramming. We conclude that human somatic cells can be faithfully reprogrammed to pluripotency by SCNT with the potential to satisfy the clinical requirements for cell replacement therapies. Bisulphite converted DNAs of two IVF-ESCs, two sendai produced iPSC lines, two retro-virus produced iPSC lines, four NT-ESCs, and the parental fibroblast were hybridized to the Illumina Infinium HumanMethylation 450K Beadchip
Project description:Banking of high-quality placental tissue specimens will enable biomarker discovery and molecular studies on diseases involving placental dysfunction. Systematic studies aimed at developing feasible standardized methodology for placental collection for genomic analyses are lacking. To determine the acceptable timeframe for placental collection, we collected multiple samples from first and third trimester placentas at serial time points 0-120 minutes after delivery, simultaneously comparing the traditional snap-freeze technique to collection in commercial solutions designed to preserve RNA (RNAlaterTM, Ambion), and DNA (DNAgard®, Biomatrica). The performance of RNAlater for preserving DNA was also tested. Nucleic acid quality was assessed by determining the RNA integrity number (RIN) and genome-wide expression and DNA methylation microarray profiling. We found that samples collected in RNAlater had higher and more consistent RINs compared to snap frozen tissue, with similar RINs obtained for tissue collected in RNAlater as large (1 cm3) and small (~0.1 cm3) tissue pieces. RNAlater appeared to better stabilize the time zero gene expression pattern compared to snap freezing for first trimester placenta. Microarray DNA methylation analysis showed that overall the DNA methylation profiles remained quite stable over a two hour time period after removal of the placenta from the uterus, with the DNAgard condition being superior to both snap freezing and RNAlater. The collection of placental samples in RNAlater and DNAgard is simple, and eliminates the need for liquid nitrogen or a freezer on-site. Moreover, the quality of the nucleic acids and the resulting data from samples collected in these preservation solutions is actually higher than that from samples collected using the traditional snap-freeze method. Thus, this new approach to placental sample collection is both easier to implement in busy clinical environments and yields higher quality data. 48 samples In this study, our objective was to identify the optimal timing and mode of collection for nucleic acids of sufficient quality to perform genome-wide RNA gene expression and DNA methylation studies for downstream molecular and functional enrichment analysis. To do this, we evaluated three different placenta collection methods: snap freezing in liquid nitrogen, RNAlaterTM, and DNAgard, over a two-hour window upon removal from the uterus, to determine: 1) the optimal collection method(s) for evaluation of mRNA expression and DNA methylation; and 2) the time period after delivery during which such optimal samples should be collected.
Project description:Genome wide DNA methylation profiling of normal whole blood samples. The data consist of 100 samples with Illumina HumanMethylation450 BeadChip data. Bisulphite converted DNA from the 100 samples were hybridized to the Illumina HumanMethylation450 BeadChip
Project description:Whole transcriptome expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and transcriptome-wide expression in G1 phase. Expression data were processed with Tiling Array Software (TAS). We analyzed one Affymetrix Human Tiling 1.0R set