Genome-wide bisulfite sequencing reveals enhancer as main target of DNA methyltion in neural conversion [Bisulfite-seq]
ABSTRACT: Genome-wide bisulfite sequencing and corresponding transcriptome are analyzed together to seek for methylation target during neural differentiation H1 human embryonic stem cells are able to differentiated into neural stem cells with induction of compound C in 72h. We extracted genomic DNA from 0, 24, 48h samples during induction and measured their DNA methylation level by BS-seq.
Project description:Arabidopsis msh1 mutants display developmental reprogramming (dr) phenotypes, include reduction in growth, enhanced branching, and delayed maturation and flowering time. MSH1-epi lines were derived by crossing MSH-dr lines with Col-0 wild type, followed by selection for homozygous MSH1/MSH1 F2 plants and serial self-pollination. MSH1-epiF3 plants displayed phenotypic variation in plant growth, showing enhanced growth, larger rosette diameter, thicker floral stems and earlier flowering time. We carried bisulfite sequencing and uncover the methylome changes accompany the heritable MSH1-epi phenotypes that condition dramatic variation in plant growth. 3 samples examined: wild type, Msh1-epiF3, msh1 mutant
Project description:Analysis of binding profile of the Polycomb group protein Ph and of GlcNAc sites in Drosophila melanogaster larvae. <br><br>Note some of the protocols for this experiment were changed in May 2010.
Project description:Transcription profiling of fission yeast /yox1/ deletion and genome wide location analysis of Yox1p and Cdc10p transcription factors reveal a negative feedback interaction: /yox1 /is transcriptionally activated by MBF, and Yox1p in turn transcriptionally represses the MBF target genes (including /yox1 /itself).
Project description:We report a single-cell whole-genome bisulfite sequencing method (scBS-Seq) capable of accurately measuring DNA methylation at up to 36% of CpGs. We observed that ESCs grown in serum/LIF or 2i/LIF both display epigenetic heterogeneity, with “2i-like” cells present in serum cultures. In silico integration of 12 individual MII oocytes datasets recapitulates the whole DNA methylome, making scBS-Seq a versatile tool to explore DNA methylation in rare cells and heterogeneous populations. scBS-Seq has been performed on mouse MII oocytes for technical validation and on mouse ESCs cultured in 2i/LIF and serum/LIF to investage epigenetic heterogeneity
Project description:Three oesophageal tissue derived cell lines, one from a normal tissue (HET1A) and two from tumour tissues (OE33 and OE199) were mixed with same number of each cell type in the same tube to get a mixed population. The C1 platform (Fluidigm) was used to capture single-cells and scATAC-seq protocols from Fluidigm ScriptHub is then used to generate the sequencing library. A single-cell ATAC-seq Bioinformatics pipeline is then developed to deconvolute the cells into their respective cell types.
Project description:Mtb appears to have developed specialized biomolecular infrastructure to survive and persist within granulomas, where it is subjected to a diverse set of stress conditions. One of these stress conditions is hypoxia. We hypothesized that host cell response is radically altered with hypoxia stressed Mtb and designed in-vitro experiments to study this phenomenon. Hypoxia-stressed as well as aerobically grown Mtb were used to infect rhesus macaque bone marrow derived macrophages (Rh-BMDMs) and the host global transcriptional response compared. Using 4 x44 k Agilent arrays specific for rhesus macaque genome, we tested in biological duplicate the effect of aerogically grown Mtb on rhesus macaque BMDMs and compared this to the corresponding effect of the hypoxia-conditioned Mtb on rhesus macaque BMDMs