A Scalable Epitope Tagging Approach for High Throughput ChIP-seq Analysis
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Jian Yan
PROVIDER: E-GEOD-78064 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:A Scalable Epitope Tagging Approach for High Throughput ChIP-seq Analysis
2016-09-01 | GSE78064 | GEO
Project description:Gene editing in induced pluripotent stem (iPS) cells has been hailed for enabling new cell therapies for various monogenetic diseases including dystrophic epidermolysis bullosa(DEB). However, manufacturing, efficacy, and safety roadblocks have limited the development of genetically corrected, autologous iPS cell-based therapies. We developed Dystrophic Epidermolysis Bullosa Cell Therapy (DEBCT), a new generation GMP-compatible (cGMP), reproducible, and scalable platform to produce autologous clinical-grade iPS cell-derived organotypic induced skin composite (iSC) grafts to treat incurable wounds of patients lacking type VII collagen (C7).
2024-06-30 | GSE229920 | GEO
Project description:Traditional sources of NK cells, such as peripheral blood, are limited by availability and donor variability. Additionally, in vitro expansion can lead to functional exhaustion and gene editing challenges. This study aims to harness iPSC technology to provide a consistent and scalable source of NK cells, overcoming the limitations of traditional sources and enhancing the potential for cancer immunotherapy applications.
2024-09-13 | GSE271952 | GEO
Project description:Advances in single-cell genomics enable commensurate improvements in methods for uncovering lineage relations among individual cells. Current sequencing based methods for cell lineage analysis depend on low resolution bulk analysis or rely on extensive single cell sequencing which is not scalable and could be biased by functional dependencies. Here we show an integrated biochemical-computational platform for generic single-cell lineage analysis that is retrospective, cost-effective and scalable. It consists of a biochemical-computational pipeline that inputs individual cells, produces targeted single-cell sequencing data and uses it to generate a lineage tree of the input cells. We validated the platform by applying it to cells sampled from an ex vivo grown tree and analyzed its feasibility landscape by computer simulations. We conclude that the platform may serve as a generic tool for lineage analysis and thus pave the way towards large-scale human cell lineage discovery.
2016-04-18 | E-MTAB-4553 | biostudies-arrayexpress
Project description:Efforts to examine the utility of alternate modalities for genetic results disclosure has widespread implications for how precision medicine research might yield direct health benefits for study participants. This study will examine the efficacy of an online self-guided program to return genetic results to a racial minority cohort population. Study results will provide empirical evidence on the effectiveness of alternate modalities for genetic results return, inform ongoing efforts to establish scalable approaches for effective return of genetic research results, and increase access to personal health information among African American women.
| 2340707 | ecrin-mdr-crc
Project description:Eukaryotic transcriptional factors (TFs) typically recognize short genomic sequences alone or together with other proteins to modulate gene expression. Mapping of TF-DNA interactions in the genome is crucial for understanding the gene regulatory programs in cells. While chromatin immunoprecipitation followed by sequencing (ChIP-Seq) is commonly used for this purpose, its application is severely limited by the availability of suitable antibodies for TFs. To overcome this limitation, we developed an efficient and scalable strategy named cmChIP-Seq that combines the clustered regularly interspaced short palindromic repeats (CRISPR) technology with microhomology mediated end joining (MMEJ) to genetically engineer a TF with an epitope tag. We demonstrated the utility of this tool by applying it to four TFs in a human colorectal cancer cell line. The highly scalable procedure makes this strategy ideal for ChIP-Seq analysis of TFs in diverse species and cell types.
| S-EPMC5536957 | biostudies-literature
Project description:One of the first steps in understanding a protein's function is to determine its localization; however, the methods for localizing proteins in some systems have not kept pace with the developments in other fields, creating a bottleneck in the analysis of the large datasets that are generated in the post-genomic era. To address this, we developed tools for tagging proteins in trypanosomatids. We made a plasmid that, when coupled with long primer PCR, can be used to produce transgenes at their endogenous loci encoding proteins tagged at either terminus or within the protein coding sequence. This system can also be used to generate deletion mutants to investigate the function of different protein domains. We show that the length of homology required for successful integration precluded long primer PCR tagging in Leishmania mexicana. Hence, we developed plasmids and a fusion PCR approach to create gene tagging amplicons with sufficiently long homologous regions for targeted integration, suitable for use in trypanosomatids with less efficient homologous recombination than Trypanosoma brucei. Importantly, we have automated the primer design, developed universal PCR conditions and optimized the workflow to make this system reliable, efficient and scalable such that whole genome tagging is now an achievable goal.
| S-EPMC4313374 | biostudies-literature
Project description:A central challenge of the postgenomic era is to comprehensively characterize the cellular role of the ?20,000 proteins encoded in the human genome. To systematically study protein function in a native cellular background, libraries of human cell lines expressing proteins tagged with a functional sequence at their endogenous loci would be very valuable. Here, using electroporation of Cas9 nuclease/single-guide RNA ribonucleoproteins and taking advantage of a split-GFP system, we describe a scalable method for the robust, scarless, and specific tagging of endogenous human genes with GFP. Our approach requires no molecular cloning and allows a large number of cell lines to be processed in parallel. We demonstrate the scalability of our method by targeting 48 human genes and show that the resulting GFP fluorescence correlates with protein expression levels. We next present how our protocols can be easily adapted for the tagging of a given target with GFP repeats, critically enabling the study of low-abundance proteins. Finally, we show that our GFP tagging approach allows the biochemical isolation of native protein complexes for proteomic studies. Taken together, our results pave the way for the large-scale generation of endogenously tagged human cell lines for the proteome-wide analysis of protein localization and interaction networks in a native cellular context.
| S-EPMC4922190 | biostudies-literature
Project description:This project used a custom-built capillary electrophoresis (CE) mass spectrometry (MS) platform to demonstrate the scalable analysis of proteins from single cells of varying sizes and protein content in different vertebrate biological models. Neural tissue fated giant cells were identified in cleavage-stage Xenopus laevis (frog) embryos, and 18 ng from its protein content was analyzed. From cultured primary neurons from the mouse, diluted samples containing ~125 pg of protein digest was measured, estimating to a portion of the somal protein content. Compared to traditional nano-flow liquid chromatography (nanoLC) MS, CE-MS provided higher sensitivity and faster analysis. CE-ESI-HRMS offers a viable approach for scalable single-cell proteomics.
2023-10-25 | PXD030607 | Pride
Project description:This project used a custom-built capillary electrophoresis (CE) mass spectrometry (MS) platform to demonstrate the scalable analysis of proteins from single cells of varying sizes and protein content in different vertebrate biological models. Neural tissue fated giant cells were identified in cleavage-stage Xenopus laevis (frog) embryos, and 18 ng from its protein content was analyzed. From cultured primary neurons from the mouse, diluted samples containing ~125 pg of protein digest was measured, estimating to a portion of the somal protein content. Compared to traditional nano-flow liquid chromatography (nanoLC) MS, CE-MS provided higher sensitivity and faster analysis. CE-ESI-HRMS offers a viable approach for scalable single-cell proteomics.
2022-03-02 | PXD031955 | Pride