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    Homo sapiens
    Tarjei Mikkelsen | 12/30/2014 - 12:10
    Transcription Factor Binding (ChIP-Seq)
    Illumina Genome Analyzer
    In embryonic stem (ES) cells, bivalent chromatin domains with overlapping repressive (H3 lysine 27 tri-methylation) and activating (H3 lysine 4 tri-methylation) histone modifications mark the promoters of more than 2000 genes. To gain insight into the structure and function of bivalent domains, we mapped key histone modifications and subunits of Polycomb repressive complexes 1 and 2 (PRC1 and PRC2) genomewide in human and mouse ES cells by chromatin immunoprecipitation followed by ultra high-...
    Mus musculus
    Richard A. Young | 12/31/2014 - 11:50
    Transcription Factor Binding (ChIP-Seq)
    Illumina Genome Analyzer II
    Nucleosome remodeling results in loss of histone occupancy. To gain insight into variations in H3 occupancy in different murine cell types, chromatin immunoprecipitation coupled with massive parallel sequencing (ChIP-seq) was performed to determine genome wide occupancy of H3 in ES cells, myotubes and pro-B cells. DNA was enriched by chromatin immunoprecipitation (ChIP) and analyzed by Solexa sequencing. ChIP was performed using an antibody against total H3 in murine ES cells in normal...
    Mus musculus
    Stu Orkin | 12/31/2014 - 15:17
    Transcription Profiling (RNA-Seq)
    Illumina HiSeq 2000
    RNA were extracted from FACS sorted CD71+,TER119- erythroid progenitors from control (Rcor1+/+ and Rcor1+/-) or Mutant (Rcor1-/- ) E13.5 fetal liver. Each library was made by pooling RNA from several fetal livers. Two biological replicates were made for either control or mutant condition.
    Mus musculus
    Sridhar Ramaswamy | 01/07/2015 - 11:46
    Transcription Profiling (RNA-Seq)
    Helicos HeliScope Single Molecule Sequencer
    Expression profiling of primary tumor, circulating tumor cells and ascites in a mouse model of pancreatic cancer suggested WNT signaling plays a role in pancreatic cancer metastasis. Induction of Wnt2 signaling in mouse pancreatic NB508 cells supported the hypothesis.
    Homo sapiens
    Sridhar Ramaswamy | 01/07/2015 - 16:29
    Transcription Profiling (RNA-Seq)
    Helicos HeliScope Single Molecule Sequencer
    Expression profiling of circulating tumor cells in human pancreatic cancer patients support a hypothesis that WNT signaling plays a role in pancreatic cancer metastasis.
    Mus musculus
    Yi Zhang | 01/08/2015 - 10:34
    Transcription Factor Binding (ChIP-Seq)
    Illumina Genome Analyzer
    Epigenetic modification of the mammalian genome by DNA methylation (5-methylcytosine) has a profound impact on chromatin structure, gene expression and maintenance of cellular identity. Recent demonstration that members of the Ten-eleven translocation (Tet) family proteins can convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) raised the possibility that Tet proteins are capable of establishing a distinct epigenetic state. We have recently demonstrated that Tet1 is specifically...
    Danio rerio
    Len Zon | 01/14/2015 - 16:01
    Transcription Factor Binding (ChIP-Seq)
    Illumina Genome Analyzer II
    Deletion of caudal/cdx genes alters hox gene expression and causes defects in posterior tissues and hematopoiesis. Yet, the defects in hox gene expression only partially explain these phenotypes. To gain deeper insight into Cdx4 function, we performed ChIP-seq combined with gene expression profiling in zebrafish, and identified the transcription factor spalt-like 4 (sall4) as a Cdx4 target. ChIP-seq revealed that Sall4 bound to its own gene locus and the cdx4 locus. Expression profiling showed...
    Homo sapiens
    Derrick Rossi | 01/19/2015 - 13:41
    Transcription Profiling (RNA-Seq)
    Illumina HiSeq 2000
    Reprogramming somatic cells to induced pluripotent stem cells (iPSCs) sets their identity back to an embryonic age. This presents a fundamental hurdle for modeling late-onset disorders using iPSC-derived cells. We therefore developed a strategy to induce age-like features in multiple iPSC-derived lineages and tested its impact on modeling Parkinson’s disease (PD). We first describe markers that predict fibroblast donor age and observed the loss of these age-related markers following iPSC...
    Homo sapiens
    Yi Zhang | 01/20/2015 - 09:40
    Transcription Profiling (RNA-Seq)
    Illumina HiSeq 2000
    Differentiation of functional pancreatic beta cells from human pluripotent stem cells provide a promising source for cell therapy, and should also facilitate human pancreas developmental study. To achieve robust yield of functional human beta cells, comprehensive understanding on the dynamic gene expression pattern and regulation is emergently required and novel regulators are expected to guide beta cell differentiation. Here we perform RNA-seq based transcriptome profiling using...
    Mus musculus
    Amit Sinha | 01/20/2015 - 16:57
    Transcription Profiling (RNA-Seq)
    Illumina HiSeq 2000
    Methylation of H3K79 is associated with chromatin at expressed genes, though it is unclear if this histone modification is required for transcription of all genes. Recent studies suggest that Wnt-responsive genes depend particularly on H3K79 methylation, which is catalyzed by the methyltransferase DOT1L. Human leukemias carrying MLL gene rearrangements show DOT1L-mediated H3K79 methylation and aberrant expression of leukemogenic genes. DOT1L inhibitors reverse these effects but their clinical...

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