Zebrafish Globin Locus (ChIP-seq)
Ontology highlight
ABSTRACT:
ORGANISM(S): Danio rerio
PROVIDER: GSE35874 | GEO | 2012/02/17
SECONDARY ACCESSION(S): PRJNA155707
REPOSITORIES: GEO
Similar Datasets
Project description:Genome-wide analysis of H3K4me3 modifications, Gata1 binding, and DNase I hypersensitivity sites in zebrafish adult red blood cells
2012-02-17 | GSE35875 | GEO
Project description:Genome-wide analysis of H3K4me3 modifications, Gata1 binding, and DNase I hypersensitivity sites in zebrafish adult red blood cells Zebrafish peripheral blood nuclei were isolated for DNase I hypersensitivity assays. Total DNA were purified using the Proteinase K digestion and Phenol-Chloroform extraction. Small DNase I fragments from the DNaseI treatement were enriched using a sucrose gradient. These ends were then labeled and amplified during library construction and for Solexa sequencing
2012-02-17 | E-GEOD-35875 | biostudies-arrayexpress
Project description:Genome-wide analysis of H3K4me3 modifications, Gata1 binding, and DNase I hypersensitivity sites in zebrafish adult red blood cells Zebrafish red cells from 10 adults were isolated for each ChIP-seq reaction. The red cells were cross-linked with formaldehyde for 20 min. DNA fragements bound by specific proteins were enriched by chromatin immunoprecipitation (ChIP) and analyzed by Solexa sequencing. A sample of whole cell extract (WCE) was sequenced and used as the background to determine enrichment. ChIP was performed using an antibody against total Gata1 and H3K4me3 (Millipore Cat. No. 17-614) as previously described in Lee et al 2006.
2012-02-17 | E-GEOD-35874 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE35874: Zebrafish Globin Locus (ChIP-seq) GSE35875: Zebrafish Globin Locus (DNAse) Refer to individual Series
2012-02-17 | E-GEOD-35895 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the SubSeries listed below.
2012-02-17 | GSE35895 | GEO
Project description:In this study, we have applied ChIP-Seq to identify putative regulatory elements throughout the zebrafish genome. For this purpose we identified sequences within the zebrafish genome that associate with H3K4me1 and H3K4me3, which are epigenetic modifications known to be associated with active cis-regulatory elements in other species. Determination of H3K4me1- and H3K4me3-binding sites in the zebrafish genome.
2011-02-25 | E-GEOD-20600 | biostudies-arrayexpress
Project description:Gata1+ cells isolated from control and foxo3b MO zebrafish at 24 and 48hpf were subjected to RNA-seq and related analyses. Gata1-GFP zebrafish stran was utilized, embryos were injected with foxo3b MO and standard MO at one-cell stage. Gata1+ cells were selected by FACS at 24 and 48hpf and submitted to RNA-seq and related analyses.
2015-08-04 | E-GEOD-66860 | biostudies-arrayexpress
Project description:Interplays among lineage specific nuclear proteins, chromatin modifying enzymes and the basal transcription machinery govern cellular differentiation, but their dynamics of actions and coordination with transcriptional control are not fully understood. Alterations in chromatin structure appear to establish a permissive state for gene activation at some loci but they play an integral role in activation at other loci. To determine the predominant roles of chromatin states and factor occupancy in directing gene regulation during differentiation, we mapped chromatin accessibility, histone modifications, and nuclear factor occupancy genome-wide during mouse erythroid differentiation dependent on the master regulatory transcription factor GATA1. Remarkably, despite extensive changes in gene expression, the chromatin state profiles (proportions of a gene in a chromatin state dominated by activating or repressive histone modifications) and accessibility remain largely unchanged during GATA1-induced erythroid differentiation. In contrast, gene induction and repression are strongly associated with changes in patterns of transcription factor occupancy. Our results indicate that during erythroid differentiation, the broad features of chromatin states are established at the stage of lineage commitment, largely independently of GATA1. These determine permissiveness for expression, with subsequent induction or repression mediated by distinctive combinations of transcription factors. Using ChIP-Seq technology to examine DNase hypersensitivity, three transcription factors, and four histone modifications in Gata1-null murine G1E line and rescued G1E-ER4 subline, and also two of the transcription factors in mouse primary erythroblasts. ChIP input DNA was sequenced in each cell type as controls.
2011-07-05 | E-GEOD-30142 | biostudies-arrayexpress
Project description:Genomic reprogramming and cellular dedifferentiation are critical to the success of de novo tissue regeneration in lower vertebrates such as zebrafish and axolotl. ChIP-seq of the histone modifications H3K27Ac, H3K27me3, and H3K4me3 was used to characterize early epigenetic changes in a zebrafish in vivo model of adult muscle regeneration.
2019-12-06 | GSE137304 | GEO