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GenomicsOff-Target Analysis of Zinc Finger Nucleases
Zinc Finger Nucleases (ZFNs) facilitate precise editing of DNA enabling targeted genomic modifications in vivo. ZFNs have been employed to obtain genetically modified plants and animals, and cell-based therapies utilizing ZFNs are undergoing clinical trials. However, many ZFNs display dose-dependent...
ORGANISM(S): Danio rerio 
2010-08-25 | E-GEOD-23762 | biostudies-arrayexpress
GenomicsGenomic targets of the KRAB and scan domain-containing zinc finger protein 263 (ZNF263).
Half of all human transcription factors use C2H2 zinc finger domains to specify site-specific DNA binding and yet very little is known about their role in gene regulation. Based on in vitro studies, a zinc finger code has been developed that predicts a binding motif for a particular zinc finger fact...
ORGANISM(S): Homo sapiens 
2009-12-03 | E-GEOD-19235 | biostudies-arrayexpress
TranscriptomicsTranscription profiling of Arabidopsis transgenic seedlings overexpressing MINI ZINC FINGER 1 (MIF1)
Phytohormones play crucial roles in regulating many aspects of plant development. Although much has been learned about the effects of individual hormones, cross-talk between and integration of different hormonal signals are still not well understood. We present a study of MINI ZINC FINGER 1 (MIF1), ...
ORGANISM(S): Arabidopsis thaliana 
2008-11-13 | E-GEOD-12729 | biostudies-arrayexpress
TranscriptomicsGlobal analysis of Drosophila Cys2-His2 zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants.
Cys2-His2 zinc finger proteins (ZFPs) are the largest group of transcription factors in higher metazoans. A complete characterization of these ZFPs and their associated target sequences is pivotal to fully annotate transcriptional regulatory networks in metazoan genomes. As a first step in this proc...
ORGANISM(S): synthetic construct 
2012-12-06 | E-GEOD-42709 | biostudies-arrayexpress
GenomicsGenome-wide binding profiles of an artificial zinc finger protein with or without a KLF3 functional domain
Transcription factors are often regarded as having two distinct components: a DNA binding domain (DBD) to allow binding to the regulatory region of a target gene and a trans-acting functional domain (FD) to modulate gene expression. Recently, it is becoming clear that the DBDs of transcription facto...
ORGANISM(S): Homo sapiens 
2016-01-05 | E-GEOD-69739 | biostudies-arrayexpress
TranscriptomicsHT-SELEX of recombinant C2H2 zinc finger domains of Sall4
To define the sequence preference of SALL4 C2H2 zinc finger domains, we performed SELEX coupled with high-throughput sequencing (HT-SELEX) using the purified SALL4 ZFC1, ZFC2 and ZFC4 domains combined with no protein control experiment.
ORGANISM(S): artificial sequences 
2021-01-05 | E-MTAB-9236 | biostudies-arrayexpress
TranscriptomicsSequence specificity is obtained from the majority of modular C2H2 zinc-finger arrays
C2H2 zinc fingers (C2H2-ZFs) are the most prevalent type of vertebrate DNA-binding domain, and typically appear in tandem arrays (ZFAs), with sequential C2H2-ZFs each contacting 3 (or more) sequential bases. C2H2-ZFs can be assembled in a modular fashion, providing one explanation for their remarkab...
ORGANISM(S): synthetic construct 
2010-12-02 | E-GEOD-25723 | biostudies-arrayexpress
TranscriptomicsDifferential IFNa-stimulated gene expression profiles in PLZF-inducible U937T monocyte cells
Sensitivity to Interferon (IFN) is determined by a complex coordination of genetic and environmental factors. A previous experiment using two renal cancer cell lines differing markedly in their response to IFN were analyzed for their ISG profiles in order to determine gene expression changes associa...
ORGANISM(S): Homo sapiens 
2010-05-18 | E-GEOD-16196 | biostudies-arrayexpress
TranscriptomicsZinc finger nuclease knockouts of human ADP-glucokinase
Zinc finger nucleases (ZFN) are powerful tools for editing genes in cells. Here we use ZFNs to interrogate the biological function of human ADPGK, which encodes an ADP-dependent glucokinase (ADPGK), in tumour cell lines. The hypothesis tested is that ADPGK utilises ADP to phosphorylate glucose under...
ORGANISM(S): Homo sapiens 
2012-07-19 | E-GEOD-39497 | biostudies-arrayexpress
TranscriptomicsCatabolite repression of phosphoenolpyruvate carboxykinase by a zinc finger protein under biotin- and pyruvate carboxylase-deficient conditions in Pichia pastoris
We have identified a methanol- and biotin-starvation-inducible zinc finger protein named ROP [repressor of phosphoenolpyruvate carboxykinase (PEPCK)] in the methylotrophic yeast Pichia pastoris. When P.pastoris strain GS115 (wild-type, WT) is cultured in biotin-deficient, glucose ammonium (Bio-) ...
ORGANISM(S): Pichia pastoris 
2011-10-13 | E-GEOD-32948 | biostudies-arrayexpress
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