Application Notes in Thematical Order


General Cell Culture Techniques

Cell Culture Coating (AN 08)
Making your own coating on µ-slides

Trypsination in µ-Channels (AN 06)
Removing adherently grown cells from a µ-channel after cultivation

Co-Cultivation (AN 10)
Application note for co-cultivation of two different cell types in µ-Slide 2 Well Co-Culture

Cultivation of Macrophages (AN 20)
Cultivation protocol for a murine macrophage cell line in µ-Slide VI0.4 and µ-Slide 8 well

Live / Dead Staining with FDA and PI (AN 33)
Viability staining of adherent cells, single cells embedded in extracellular matrix, and cellular clusters

Gene Transfection (AN 07)
Example showing how protocols for gene transfection can easily be adapted to the work in cell culture channels

Adenoviral Transduction of Human Cells (AN 28)
Detailed protocol for handling recombinant adenoviruses, plus designing an approach for transducing human cells

Lentiviral Transduction of Human Cells (AN 41)
Detailed protocol for handling recombinant lentiviruses, plus designing an approach for transducing human cells

Transfer of mRNA into L929 Cells using Fuse-It-mRNA
(AN 43)

Detailed instructions for the optimization of the Fuse-It-mRNA protocol for L929 Cells in the µ-Plate 24 Well

Transfer of mRNA into iPSC-derived Cardiomyocytes Using Fuse-It-mRNA (AN 29)
Detailed instructions for the optimization of the Fuse-It-mRNA protocol for iPSC-derived Cardiomyocytes in the µ-Slide VI 0.4

Western Blot Analysis with Cell Samples Grown in Channel-µ-Slides (AN 38)
Detailed protocol for performing cell lysis in channel-µ-Slides and subsequent SDS-Page with Western Blot Analysis

Gene Expression Profiling with Cell Samples Grown in Channel-µ-Slides (AN 40)
Detailed protocol for performing cell lysis in channel-µ-Slides and subsequent RNA-Isolation with RT-qPCR Analysis

Cell Proliferation Assay in µ-Slide Angiogenesis (AN 39)
A Detailed Protocol for Analyzing the Cell Proliferation Using MDCK Cells for the Example

Electrical Stimulation of Cardiomyocytes in µ-Slide I Luer Electrode (AN 47)
Typical parameters for the stimulation of cardiomyocytes using the µ-Slide I Luer Electrode as well as a seeding protocol for the cells


Chemotaxis

Chemotaxis (AN 14)
Application Note for 2D chemotactical assays using µ-Slide Chemotaxis 2D

Chemotaxis 2D and 3D (AN 17)
General protocol for 2D and 3D gel assays with µ-Slide Chemotaxis

3D Chemotaxis Protocol for Non-Adherent Cells in a Gel Matrix (AN 23)
Application Note providing a specific example protocol for chemotaxis of dendritic cells in a collagen gel

Chemotaxis Assay with Cells in the Reservoirs (AN 35)
A detailed protocol for using adherent cells as chemoattractant-producers in the large reservoirs of the µ-Slide Chemotaxis.

Chemotaxis of HT-1080 Cells in 2D and 3D (AN 24)
Detailed protocol of experimental parameters and example data of HT-1080 cells migrating in 2D and in 3D in collagen I gels

Chemotaxis of HUVEC Cells in 2D and 3D (AN 34)
Detailed protocol of experimental parameters and example data of HUVEC cells migrating in 2D and in 3D in collagen I gels.

Image Shift Correction in Microscopic Time Lapse Sequences (AN 37)
Instructions for correcting an externally generated shift of the sample  in time lapse images (e.g.  in chemotaxis experiments)


Wound Healing & Cell Migration

Wound Healing Assay (AN 21)
Setting up a wound healing assay with the ibidi Culture-Insert in a µ-Dish 35 mm

Wound Healing Assay – Data Analysis (AN 30)
Setup optimization of wound healing experiments, with instructions for data analysis and interpretation using WimScratch

Wound Healing Assay in µ-Plate 24 Well (AN 36)
A handling protocol for wound healing assays: Screening substances for pro- or anti-migrational effects


Angiogenesis

Tube Formation (AN 19)
Setting up a tube formation assay with µ-Slide Angiogenesis

Tube Formation – Assay Optimization and Data Analysis (AN 27)
Setup optimization of tube formation assays, with instructions for data analysis and interpretation

Tube Formation in µ-Plate Angiogenesis 96 well (AN 05)
Handling protocol for tube formation assays using a multi-channel pipette and the µ-Plate Angiogenesis 96 well


Cell Culture Under Flow Conditions

Growing Cells in µ-Channels (AN 03)
Growing cells inside a µ-Slide VI 0.4, and a comparison between channels and open wells

Shear Stress and Shear Rates (AN 11)
Detailed information on shear stress/shear rates and flow rates in our channel slides

Shear Stress and Shear Rates in µ-Slide µ-Shaped (AN 18)
Detailed information on shear stress/shear rates and flow rates in our µ-Slide y-shaped

HUVECs Under Perfusion (AN 13)
Setting up a flow experiment using μ-Slide I and HUVECs

Serial Connection of Flow Chambers (AN 25)
Setup protocol for connecting several Luer-Slides to one Fluidic Unit

Serial Connection of µ-Slide VI 0.4 (AN 31)
Protocol for connecting the six channels of µ-Slide VI 0.4 to one Fluidic Unit


3D Cell Culture

Collagen I Gel for 3D Cell Culture (AN 26)
Fabrication protocols for collagen I gel (bovine and rat tail) with different cell media

Generation of Spheroids (AN 32)
Generation of spheroids using the liquid overlay technique


Immunofluorescence

Mounting Medium Types (AN 45)
A comparison of non-hardening and hardening mounting media

Fluorescence Staining using a 12 Well Chamber, removable (AN 49)
A handling protocol for immunofluorescence staining in the 12 Well Chamber, removable

Fluorescence Staining using a 3 Well Chamber, removable (AN 50)
A handling protocol for immunofluorescence staining in the 3 Well Chamber, removable, including instructions for using the volume-minimizing coverslip

Fluorescence Staining using a µ-Slide I (AN 02)
Examples describing how to do immunofluorescence stainings using µ-Slides

Fluorescence Staining using a µ-Slide VI (AN 09)
Examples describing how to do immunofluorescence stainings using µ-Slides

Fluorescence Staining using a µ-Slide y-shaped (AN 15)
Examples describing how to do immunofluorescence stainings using µ-Slides

Fluorescence Staining using a µ-Slide 8 well (AN 16)
Examples describing how to do immunofluorescence stainings using µ-Slides


Microscopy and More

Pixel Size (AN 22)
Measuring and calculating the pixel size of microscopic images

Avoiding Evaporation (AN 12)
Decreasing evaporation during cell cultivation by using the ibidi humidifying chamber Olaf and µ-Slides

Gradients Inside µ-Slide I (AN 01)
Establishing a concentration profile

Lipid Monolayer (AN 04)
Description of the uncomplicated and fast preparation of a lipid monolayer on uncoated slides