Zebrafish Globin Locus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA151955 | ENA |
REPOSITORIES: ENA
Similar Datasets
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: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:Human embryonic stem cells provide an alternative to using human embryos for studying developmentally regulated gene expression. The co-expression of high levels of embryonic epsilon and fetal gamma globin by the hESC-derived erythroblasts allows the interrogation of epsilon globin regulation at the transcriptional and epigenetic level which could only be attained previously by studying cell lines or transgenic mice. In this study, we compared the histone modifications across the beta globin locus of the undifferentiated hESCs and hESC-, FL-, and mobilized PB CD34+ cells-derived erythroblasts, which have distinct globin expression patterns corresponding to their developmental stages. We demonstrated that the histone codes employed by the beta globin locus are conserved throughout development. Furthermore, in spite of the close proximity of the epsilon globin promoter, as compared to the gamma or beta globin promoter, with the LCR, a chromatin loop was also formed between the LCR and the active epsilon globin promoter, similar to the loop that forms between the gamma or beta globin promoters and the LCR, in contrary to the previously proposed tracking mechanism. Human embryonic stem cells, hESC-, FL-, and PB derived erythroblasts were studied. The enrichment of H3K4me3 and AcH3 acrossed the beta globin locus was studied using ChIP-seq.
2015-01-26 | E-GEOD-35375 | 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: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
2012-02-17 | GSE35874 | GEO
Project description:Human embryonic stem cells provide an alternative to using human embryos for studying developmentally regulated gene expression. The co-expression of high levels of embryonic epsilon and fetal gamma globin by the hESC-derived erythroblasts allows the interrogation of epsilon globin regulation at the transcriptional and epigenetic level which could only be attained previously by studying cell lines or transgenic mice. In this study, we compared the histone modifications across the beta globin locus of the undifferentiated hESCs and hESC-, FL-, and mobilized PB CD34+ cells-derived erythroblasts, which have distinct globin expression patterns corresponding to their developmental stages. We demonstrated that the histone codes employed by the beta globin locus are conserved throughout development. Furthermore, in spite of the close proximity of the epsilon globin promoter, as compared to the gamma or beta globin promoter, with the LCR, a chromatin loop was also formed between the LCR and the active epsilon globin promoter, similar to the loop that forms between the gamma or beta globin promoters and the LCR, in contrary to the previously proposed tracking mechanism.
2015-01-26 | GSE35375 | GEO
Project description:We have engineered the 3 prime HS1 CTCF binding site at the human beta globin gene locus in HUDEP-2 cells and performed RNA-seq/ChIP-seq/ATAC-seq as well as HiC and capture HiC to dissect its potential in regulating gene expression
2020-10-30 | GSE160424 | GEO
Project description:We have engineered the 3 prime HS1 CTCF binding site at the human beta globin gene locus in HUDEP-2 cells and performed RNA-seq/ChIP-seq/ATAC-seq as well as HiC and capture HiC to dissect its potential in regulating gene expression
2020-10-30 | GSE160423 | GEO
Project description:We have engineered the 3 prime HS1 CTCF binding site at the human beta globin gene locus in HUDEP-2 cells and performed RNA-seq/ChIP-seq/ATAC-seq as well as HiC and capture HiC to dissect its potential in regulating gene expression
2020-10-30 | GSE160421 | GEO