TrAEL-seq for CUP1 locus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA693455 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13489210.fastq.gz | Fastqsanger.gz | |||
| SRR13489211.fastq.gz | Fastqsanger.gz | |||
| SRR13489212.fastq.gz | Fastqsanger.gz | |||
| SRR13489213.fastq.gz | Fastqsanger.gz | |||
| SRR13489214.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 22 |
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:Expression of Shh in the limb is dependent on a distant enhancer located 850kb away from the gene promoter. We performed chromatin conformation capture (4C-Seq) analysis of the Shh locus in E11.5 mouse limbs so as to better understand the relationship between this regulatory interaction and the structural organisation of the locus. The experiments were performed on wild-type animals as well as on animals carrying an engineered chromosomal inversion (INV(6-C2) (INV6)) . The different viewpoints used (Shh, ZRS, Nom1, Rbm33, Rnf32) enable to characterize the 3D organisation of the locus in the different contexts. The inversion INV6 disrupts the normal topological organisation of the Shh locus in a compact 3D-domain and prevents the physical and regulatory interaction between Shh and its limb enhancer, even though the genomic distance separating the two elements is reduced compared to WT.
2017-01-12 | E-MTAB-4980 | biostudies-arrayexpress
Project description:Arsenic exposure is a global health problem. Millions of people encounter arsenic through contaminated drinking water, consumption, and inhalation. The arsenic response locus in budding yeast is responsible for the detoxification of arsenic and its removal from the cell. This locus constitutes a conserved pathway ranging from prokaryotes to higher eukaryotes. The goal of this study was to identify how the arsenic response locus is regulated in an arsenic dependent manner. An affinity enrichment strategy called CRISPR-Chromatin Affinity Purification with Mass Spectrometry (CRISPR-ChAP-MS) was used that provides for the proteomic characterization of a given locus. CRISPR-ChAP-MS was applied to the arsenic response locus and uncovered 40 nuclear-annotated proteins showing enrichment. Functional assays, identified the histone acetyltransferase activity of SAGA and the ATPase chromatin remodeling activity of SWI/SNF to be required for activation of the locus. Furthermore, SAGA and SWI/SNF were both found to specifically organize the chromatin structure at the arsenic response locus for activation of gene transcription. This study provides the first proteomic characterization of an arsenic response locus and key insight into the mechanism of transcriptional activation that is necessary for detoxification of arsenic from the cell.
2020-05-07 | PXD009902 | Pride
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
Project description:We set out to develop an unbiased, genome-wide method to screen for proteins that locate to the OCT4 proximal enhancer (PE) in hESCs; for this purpose, we developed an optimized locus-specific proteomics approach in hESCs. First, we designed TALEN (Transcription Activator-Like Effector Nuclease) constructs to target the sequences that are near the OCT4 PE, located in a region of DNaseI hypersensitivity. TALEN constructs with the highest cutting efficiency were chosen for locus-specific proteomics. We then made modifications to the original TALEN protein to transform it into a catalytically-dead TALE (dTALE) protein that is optimized for locus-specific proteomics in hESCs via three steps: 1) The nuclease-domain FokI at the C-terminus was replaced by a GFP (green fluorescence protein); 2) a 3X FLAG tag at the N-terminus was included for following pull-down analysis; 3) the existing CMV promoter was replaced with an EF1alpha promoter that has robust expression in hESCs. This dTALE protein could then be chemically crosslinked to the OCT4 locus together with all the other proteins that bind to the locus. We verified that dTALE protein binds to the targeted locus by chromatin immunoprecipitation (ChIP)-qPCR. Following crosslinking, chromatin was sheared, and all the associated proteins were immunoprecipitated using an anti-FLAG antibody. Immunoprecipitation pulled down the dTALE protein as well as other proteins and complexes that are also attached to that region. Crosslinking was then reversed, and the samples were subjected to mass spectrometry to enable generation of a list of proteins that potentially bind to OCT4 PE locus.
2019-01-07 | PXD010963 | Pride
Project description:LsRP based on amino acid locus information and Support Vector Regression can be used to predict peptide retention time in LC-MS experiments.
2017-04-10 | PXD005572 | Pride
Project description:This dataset contains ploy-A tailed enriched RNA-seq data obtained from single cell-derived control and CRISPR/Cas9 induced tRNA gene deletion clones in the human cancer cell line HAP1. In this study, we found a large genomic deletion of the 10q23 locus in our Cas9 modified clones and further investigate the effect on the transcriptome.
2023-10-24 | E-MTAB-11858 | biostudies-arrayexpress
Project description:Chromosome Conformation Capture (4C seq) at the rs9929218 locus in colorectal cancinogensis
2020-10-01 | GSE121623 | 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. 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