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GenomicsGC-rich Sequence Elements Recruit Polycomb Repressive Complex 2 (PRC2) in ES cells
Polycomb proteins are epigenetic regulators that localize to developmental loci in the early embryo where they mediate lineage-specific gene repression. In Drosophila, these repressors are recruited to sequence elements by DNA binding proteins associated with Polycomb repressive complex 2 (PRC2). Ho...
ORGANISM(S): Mus musculus 
2010-11-23 | E-GEOD-25197 | biostudies-arrayexpress
GenomicsChromatin Profiling by Directly Sequencing Small Quantities of Immunoprecipitated DNA
Chromatin structure and transcription factor localization can be assayed genome-wide by sequencing genomic DNA fractionated by protein occupancy or other properties. However, current technologies involve multiple steps that introduce bias and inefficiency. Here we apply a single-molecule approach to...
ORGANISM(S): Mus musculus 
2009-11-29 | E-GEOD-18699 | biostudies-arrayexpress
GenomicsGenome-wide Chromatin Maps Derived from Limited Numbers of Hematopoietic Progenitors
Whole genome mapping of protein-DNA interactions can be performed by coupling chromatin immunoprecipitation (ChIP) with high-throughput sequencing (ChIP-Seq). However, current methods require large amounts of starting materials which precludes their application to rare cell types. Here, we combine a...
ORGANISM(S): Mus musculus 
2010-07-01 | E-GEOD-22075 | biostudies-arrayexpress
GenomicsCombinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells
Hundreds of Chromatin Regulators (CRs) control chromatin structure and function by catalyzing and binding histone modifications, yet the rules governing these key processes remain obscure. Here, we present a systematic approach to infer CR function. We developed ChIP-string, a meso-scale assay that ...
ORGANISM(S): Homo sapiens 
2011-12-23 | E-GEOD-32509 | biostudies-arrayexpress
GenomicsGenome-wide chromatin maps of T-cell acute lymphoblastic leukemia (T-ALL) [ChIP-seq]
Here we modeled T-ALL resistance to Notch inhibition, identifying M-bM-^@M-^XpersisterM-bM-^@M-^Y cells that readily expand in the presence of gamma secretase inhibitor (GSI) and the absence of Notch signaling. Rare persister cells are already present in naM-CM-/ve T-ALL populations, and the reversi...
ORGANISM(S): Homo sapiens 
2014-03-01 | E-GEOD-54379 | biostudies-arrayexpress
GenomicsGenome-wide maps of chromatin state in pluripotent and lineage-committed cells
Genome-wide maps of chromatin state (H3K4me3, H3K9me3, H3K27me3, H3K36me3, H4K20me3) in pluripotent and lineage-committed cells We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in mammalian cells. By obtaining over four b...
ORGANISM(S): Mus musculus 
2008-07-24 | E-GEOD-12241 | biostudies-arrayexpress
GenomicsMapping polycomb complexes in human and mouse embryonic stem cells
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 m...
ORGANISM(S): Mus musculus 
2008-11-01 | E-GEOD-13084 | biostudies-arrayexpress
GenomicsEpstein-Barr Virus Exploits Intrinsic B-Lymphocyte Transcription Programs to Achieve Immortal Cell Growth
Epstein-Barr Virus Nuclear Antigen 2 (EBNA2) gene regulation through the cell RBPJ transcription factor (TF) is essential for conversion of resting B-lymphocytes (RBLs) into Lymphoblastoid Cell Lines (LCLs). ChIP-seq investigation of EBNA2 and RBPJ sites in LCL DNA found EBNA2 at 5151 and RBPJ at 10...
ORGANISM(S): Homo sapiens 
2011-07-01 | E-GEOD-29498 | biostudies-arrayexpress
GenomicsInsights into GATA-1-Mediated Gene Activation versus Repression via Genome-wide Chromatin Occupancy Analysis
The transcription factor GATA-1 is required for terminal erythroid maturation and functions as an activator or repressor depending on gene context. Yet its in vivo site selectivity and ability to distinguish between activated versus repressed genes remain incompletely understood. In this study, we p...
ORGANISM(S): Mus musculus 
2009-11-25 | E-GEOD-16594 | biostudies-arrayexpress
ProteomicsEpigenetic Silencing by SETDB1 Suppresses Tumor-cell Intrinsic Immunogenicity
Griffin GK, Wu J, Iracheta-Vellve A, Patti JC, Hsu J, Davis T, Dele-Oni D, Du PP, Halawi A, Ishizuka JJ, Kim S, Klaeger S, Knudsen NH, Miller BC, Nguyen T, Olander K, Papanastasiou M, Rachimi S, Robitschek EJ, Schneider EM, Yeary M, Zimmer M, Jaffe JD, Carr SA, Doench JG, Haining WN, Yates KB, Mangu...
ORGANISM(S): Mus Musculus (ncbitaxon:10090) 
2020-12-11 | MSV000086580 | MassIVE
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