Dataset Information

A 3D mixing-based portable magnetic device for fully automatic immunofluorescence staining of γ-H2AX in UVC-irradiated CD4⁺ cells.

ABSTRACT: Immunofluorescence (IF) is a common method used in cell biology. The conventional protocol for IF staining is time and labor-intensive, operator dependent and reagent-consuming. Magnetic Bead (MB)-based microdevices are frequently utilized in cellular assays, but integration of simple and efficient mixing with downstream multi-step manipulation of MBs for automatic IF staining is still challenging. We herein present a portable, inexpensive and integratable device for MB-based automatic IF staining. First, a front-end cell capture step is performed using a 3D-mixing module, which is built upon a novel mechanism named ec-2MagRotors and generates periodically changing 3D magnetic fields. A 5-fold enhancement of cell capture efficiency was attained even with a low bead-to-cell concentration ratio (5 : 1), when conducting magnetic 3D mixing. Second, a 1D-moving module is employed downstream to automatically manipulate MB-cell complexes for IF staining. Further, a simplified protocol for staining of γ-H2AX, a biomarker widely used in evaluation of cell radiation damage, is presented for proof-of-principle study of the magnetic device. Using UVC-irradiated CD4⁺ cells as samples, our device achieved fully automatic γ-H2AX staining within 40 minutes at room temperature and showed a linear dose-response relationship. The developed portable magnetic device is automatic, efficient, cost-effective and simple-to-use, holding great potential for applications in different IF assays.

SUBMITTER: Zhong R

PROVIDER: S-EPMC9055984 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature

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A 3D mixing-based portable magnetic device for fully automatic immunofluorescence staining of γ-H2AX in UVC-irradiated CD4<sup>+</sup> cells.

Zhong Runtao R Hou Liangsheng L Zhao Yingbo Y Wang Tianle T Wang Shaohua S Wang Mengyu M Xu Dan D Sun Yeqing Y

RSC advances 20200807 49

Immunofluorescence (IF) is a common method used in cell biology. The conventional protocol for IF staining is time and labor-intensive, operator dependent and reagent-consuming. Magnetic Bead (MB)-based microdevices are frequently utilized in cellular assays, but integration of simple and efficient mixing with downstream multi-step manipulation of MBs for automatic IF staining is still challenging. We herein present a portable, inexpensive and integratable device for MB-based automatic IF staini ...[more]

PMID: 35521108

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Project description:The improvement of sequencing technologies has facilitated generalization of metagenomic sequencing, which has become a standard procedure for analyzing the structure and functionality of microbiomes. Bioinformatic analysis of sequencing results poses a challenge because it involves many different complex steps. SqueezeMeta is a fully automatic pipeline for metagenomics/metatranscriptomics, covering all steps of the analysis. SqueezeMeta includes multi-metagenome support that enables co-assembly of related metagenomes and retrieval of individual genomes via binning procedures. SqueezeMeta features several unique characteristics: co-assembly procedure or co-assembly of unlimited number of metagenomes via merging of individual assembled metagenomes, both with read mapping for estimation of the abundances of genes in each metagenome. It also includes binning and bin checking for retrieving individual genomes. Internal checks for the assembly and binning steps provide information about the consistency of contigs and bins. Moreover, results are stored in a MySQL database, where they can be easily exported and shared, and can be inspected anywhere using a flexible web interface that allows simple creation of complex queries. We illustrate the potential of SqueezeMeta by analyzing 32 gut metagenomes in a fully automatic way, enabling retrieval of several million genes and several hundreds of genomic bins. One of the motivations in the development of SqueezeMeta was producing a software capable of running in small desktop computers and thus amenable to all users and settings. We were also able to co-assemble two of these metagenomes and complete the full analysis in less than one day using a simple laptop computer. This reveals the capacity of SqueezeMeta to run without high-performance computing infrastructure and in absence of any network connectivity. It is therefore adequate for in situ, real time analysis of metagenomes produced by nanopore sequencing. SqueezeMeta can be downloaded from https://github.com/jtamames/SqueezeMeta.

Dataset Information

A 3D mixing-based portable magnetic device for fully automatic immunofluorescence staining of γ-H2AX in UVC-irradiated CD4⁺ cells.

Publications

A 3D mixing-based portable magnetic device for fully automatic immunofluorescence staining of γ-H2AX in UVC-irradiated CD4<sup>+</sup> cells.

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OmicsDI is part of the ELIXIR infrastructure

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Dataset Information

A 3D mixing-based portable magnetic device for fully automatic immunofluorescence staining of γ-H2AX in UVC-irradiated CD4+ cells.

Publications

A 3D mixing-based portable magnetic device for fully automatic immunofluorescence staining of γ-H2AX in UVC-irradiated CD4<sup>+</sup> cells.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets

A 3D mixing-based portable magnetic device for fully automatic immunofluorescence staining of γ-H2AX in UVC-irradiated CD4⁺ cells.