Dataset Information

"Chip-on-a-Transwell" Devices for User-Friendly Control of the Microenvironment of Cultured Cells.

ABSTRACT: We present microfabricated poly(dimethylsiloxane) templates assembled atop Transwell membranes ("Chip-on-a-Transwell") for focal delivery of soluble reagents to cells. This modified Transwell operates based on area-selective diffusion of soluble species to the basal side of cells. The device was capable of addressing small groups of cells, with a maximum spatial resolution of 20 μm, while sustaining focal signal for up to 48 hours. Furthermore, we developed a fluorosilane-based cell micropatterning method that complements the Transwell system, creating well-defined arrays of muscle cell cultures and enabling automated microscopy and image analysis protocols. The micropatterning method is based on plasma-etching hydrophilic cell-adhesive tracks against a hydrophobic fluorosilane cell-repellent background. We applied the platform as a model of the neuromuscular junction (NMJ), in which we effectively substituted motor neurons with apertures delivering agrin stimuli to subcellular regions of micropatterned myotubes. With the Transwell system, we demonstrated that focal agrin application to subcellular sections of myotubes induced localized acetylcholine receptor microclustering, mimicking the in vivo NMJ. We also demonstrated spatially selective transfection of a monolayer of cells using Lipofectamine carrying the plasmid DNA for pMax GFP, which is ubiquitously expressed in transfected cells. In summary, we present a user-friendly cell culture tool that provides spatiotemporal control of the fluidic and substrate microenvironments with potential applications to developmental biology and tissue engineering.

SUBMITTER: Cheng JW

PROVIDER: S-EPMC8852363 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

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"Chip-on-a-Transwell" Devices for User-Friendly Control of the Microenvironment of Cultured Cells.

Cheng Jonathan W JW Sip Christopher G CG Lindstedt Philip R PR Boitano Ross R Bluestein Blake M BM Gamble Lara J LJ Folch Albert A

ACS applied bio materials 20191021 11

We present microfabricated poly(dimethylsiloxane) templates assembled atop Transwell membranes ("Chip-on-a-Transwell") for focal delivery of soluble reagents to cells. This modified Transwell operates based on area-selective diffusion of soluble species to the basal side of cells. The device was capable of addressing small groups of cells, with a maximum spatial resolution of 20 μm, while sustaining focal signal for up to 48 hours. Furthermore, we developed a fluorosilane-based cell micropattern ...[more]

PMID: 35021498

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Project description:Comparative co-localization analysis of transcription factors (TFs) and epigenetic marks (EMs) in specific biological contexts is one of the most critical areas of ChIP-Seq data analysis beyond peak calling. Yet there is a significant lack of user-friendly and powerful tools geared towards co-localization analysis based exploratory research. Most tools currently used for co-localization analysis are command line only and require extensive installation procedures and Linux expertise. Online tools partially address the usability issues of command line tools, but slow response times and few customization features make them unsuitable for rapid data-driven interactive exploratory research. We have developed PAPST: Peak Assignment and Profile Search Tool, a user-friendly yet powerful platform with a unique design, which integrates both gene-centric and peak-centric co-localization analysis into a single package. Most of PAPST's functions can be completed in less than five seconds, allowing quick cycles of data-driven hypothesis generation and testing. With PAPST, a researcher with or without computational expertise can perform sophisticated co-localization pattern analysis of multiple TFs and EMs, either against all known genes or a set of genomic regions obtained from public repositories or prior analysis. PAPST is a versatile, efficient, and customizable tool for genome-wide data-driven exploratory research. Creatively used, PAPST can be quickly applied to any genomic data analysis that involves a comparison of two or more sets of genomic coordinate intervals, making it a powerful tool for a wide range of exploratory genomic research. We first present PAPST's general purpose features then apply it to several public ChIP-Seq data sets to demonstrate its rapid execution and potential for cutting-edge research with a case study in enhancer analysis. To our knowledge, PAPST is the first software of its kind to provide efficient and sophisticated post peak-calling ChIP-Seq data analysis as an easy-to-use interactive application. PAPST is available at https://github.com/paulbible/papst and is a public domain work.

Dataset Information

"Chip-on-a-Transwell" Devices for User-Friendly Control of the Microenvironment of Cultured Cells.

Publications

"Chip-on-a-Transwell" Devices for User-Friendly Control of the Microenvironment of Cultured Cells.

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