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ATAC-Seq of a Single Myofiber from Mus musculus

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From 3D to 2D: Harmonization of Protocols for Two-dimensional Cultures on Cell Culture Inserts of Intestinal Organoids from Various Species

Authors: David Warschkau, Estefanía Delgado-Betancourt, David Holthaus, Antonia Müller, Gudrun Kliem, Susanne M. Krug, Joerg-Dieter Schulzke, Toni Aebischer, Christian Klotz and Frank Seeber, date: 01/20/2022, view: 1304, Q&A: 0

[Abstract]

In the expanding field of intestinal organoid research, various protocols for three- and two-dimensional organoid-derived cell cultures exist. Two-dimensional organoid-derived monolayers are used to overcome some limitations of three-dimensional organoid cultures. They are increasingly used also in infection research, to study physiological

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Fluidigm Based Single-cell Gene Expression Library Preparation from Patient-derived Small Intestinal Organoids

Authors: Kohei Suzuki and Ryuichi Okamoto, date: 10/05/2020, view: 2589, Q&A: 0

[Abstract] In this protocol, we describe our methods to isolate crypts from patients' biopsy samples and to culture human intestinal stem cells as it’s called “organoid.” Beyond that, we describe how to dissociate organoids cells into single cells for single-cell analysis as a further application. This protocol should provide investigators sufficient tools ...

Gene Expression Analysis of Sorted Cells by RNA-seq in Drosophila Intestine

Authors: Jun Chen, Jia Li, Huaiwei Huang and Rongwen Xi, date: 12/20/2016, view: 13550, Q&A: 1

[Abstract] RNA sequencing (RNA-seq) has become a popular method for profiling gene expression. Among many applications, one common purpose is to identify differentially expressed genes and pathways in different biological or pathological conditions. This protocol provides detailed procedure for RNA-seq analysis of ~250,000 sorted Drosophila ...

Immunofluorescent Staining of Mouse Intestinal Stem Cells

Authors: Kevin P. O’Rourke, Lukas E Dow and Scott W Lowe, date: 02/20/2016, view: 30084, Q&A: 1

[Abstract] Immunofluorescent staining of organoids can be performed to visualize molecular markers of cell behavior. For example, cell proliferation marked by incorporation of nucleotide (EdU), or to observe markers of intestinal differentiation including paneth cells, goblet cells, or enterocytes (see Figure 1). In this protocol we detail a method to fix, ...

Isolation, Culture, and Maintenance of Mouse Intestinal Stem Cells

Authors: Kevin P. O’Rourke, Sarah Ackerman, Lukas E Dow and Scott W Lowe, date: 02/20/2016, view: 25513, Q&A: 6

[Abstract] In this protocol we describe our modifications to a method to isolate, culture and maintain mouse intestinal stem cells as crypt-villus forming organoids. These cells, isolated either from the small or large intestine, maintain self-renewal and multilineage differentiation potential over time. This provides investigators a tool to culture wild ...

Isolation and Flow-cytometric Analysis of Mouse Intestinal Crypt Cells

Authors: Dayanira Alsina-Beauchamp, Paloma del Reino and Ana Cuenda, date: 11/05/2015, view: 14340, Q&A: 0

[Abstract] The intestinal epithelial layer forms tubular invaginations into the underlying connective tissue of the lamina propria. These structures, termed crypts, are the basic functional unit of the intestine. Colon crypts and the surrounding lamina propria house different cell types, including epithelial cells, stem cells, enterocytes, goblet cells, as ...

Immunolabelling of Thin Slices of Mouse Descending Colon and Jejunum

Authors: Julien Bellis, Isabelle Duluc, Jean-Noël Freund and Jan R. De Mey, date: 10/20/2013, view: 8851, Q&A: 0

[Abstract] This protocol describes a method for efficient immunolabelling of thin tissue slices containing a few rows of intact intestinal crypts, which yields large numbers of them being oriented favorably for recording stacks of optical sections aligned with the crypt long axis (Bellis et al., 2012). The latter can then be used for cell positional ...

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