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GenomicsA genome-wide analysis of Cas9 binding specificity using ChIP-seq and targeted sequence capture
Clustered regularly interspaced short palindromic repeat (CRISPR) RNA-guided nucleases have gathered considerable excitement as a tool for genome engineering. However, questions remain about the specificity of their target site recognition. Most previous studies have examined predicted off-target bi...
ORGANISM(S): Homo sapiens 
2015-03-04 | E-GEOD-61099 | biostudies-arrayexpress
GenomicsSpark: A navigational paradigm for genomic data exploration
Biologists possess the detailed knowledge critical for extracting biological insight from genome-wide data resources and yet they are increasingly faced with non-trivial computational analysis challenges posed by genome-scale methodologies. To lower this computational barrier, particularly in the ea...
ORGANISM(S): Homo sapiens 
2012-11-06 | E-GEOD-39096 | biostudies-arrayexpress
TranscriptomicsUsing ChIP-chip technology to reveal common principles of transcriptional repression in normal and cancer cells
We compared 12 different cell populations, including embryonic stem cells before and during differentiation into embryoid bodies as well as various types of normal and tumor cells to determine if pluripotent vs. differentiated cell types use different mechanisms to establish their transcriptome. We ...
ORGANISM(S): Mus musculus 
2008-03-31 | E-GEOD-10504 | biostudies-arrayexpress
TranscriptomicsGlobal analysis of ZNF217 chromatin occupancy in the breast cancer cell genome reveals an association with Eralpha
Background: The ZNF217 gene, encoding a C2H2 zinc finger protein, is located at 20q13 and found amplified and overexpressed in greater than 20% of breast tumors. Current studies indicate ZNF217 drives tumorigenesis, yet the regulatory mechanisms of ZNF217 are largely unknown. Because ZNF217 associat...
ORGANISM(S): Homo sapiens 
2014-06-15 | E-GEOD-58326 | biostudies-arrayexpress
GenomicsAutophagy driven by a master regulator of hematopoiesis
Developmental and homeostatic remodeling of cellular organelles is mediated by a complex process termed autophagy. The cohort of proteins that constitute the autophagy machinery function in a multistep biochemical pathway. Though components of the autophagy machinery are broadly expressed, autophagy...
ORGANISM(S): Homo sapiens 
2011-09-30 | E-GEOD-32491 | biostudies-arrayexpress
GenomicsGenome-wide binding of the orphan nuclear receptor TR4 suggests its general role in fundamental biological processes
The orphan nuclear receptor TR4 (human testicular receptor 4 or NR2C2) plays a pivotal role in a variety of biological and metabolic processes. With no known ligand and few known target genes, the mode of TR4 function was unclear. We report the first genome-wide identification and characterization o...
ORGANISM(S): Homo sapiens 
2010-11-15 | E-GEOD-24685 | biostudies-arrayexpress
GenomicsGenetic Framework for GATA Factor Function in Vascular Biology
Vascular endothelial dysfunction underlies the genesis and progression of numerous diseases. Whereas the GATA transcription factor GATA-2 is expressed in endothelial cells and is implicated in coronary heart disease, it has been studied predominantly as a master regulator of hematopoiesis. As many q...
ORGANISM(S): Homo sapiens 
2011-08-11 | E-GEOD-29531 | biostudies-arrayexpress
TranscriptomicsImprovements in sample preparation for ChIP-chip assays
We have improved the new protocol for ChIP-chip by using pooling method. The new method has produced reproducible binding patterns and low background signals. We have performed and compared three methods for ChIP-chip samples: LMPCR, 10 Pooled Samples and WGA.
ORGANISM(S): Homo sapiens 
2010-07-01 | E-GEOD-5251 | biostudies-arrayexpress
GenomicsEndogenous mammalian histone H3.3 exhibits chromatin-related functions during development
Background. The histone variant H3.3 plays key roles in regulating chromatin states and transcription. However, the role of endogenous H3.3 in mammalian cells and during development has been less thoroughly investigated. To address this gap, we report the production and phenotypic analysis of mice a...
ORGANISM(S): Mus musculus 
2013-04-24 | E-GEOD-34546 | biostudies-arrayexpress
GenomicsGenome-wide maps of GATA factor occupancy in K562 cells
GATA factors interact with simple DNA motifs (WGATAR) to regulate critical processes, including hematopoiesis, but very few WGATAR motifs are occupied in genomes. Given the rudimentary knowledge of mechanisms underlying this restriction, and how GATA factors establish genetic networks, we used ChIP-...
ORGANISM(S): Homo sapiens 
2009-11-25 | E-GEOD-18868 | biostudies-arrayexpress
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