scholarly journals High-Density Cell Arrays for Genome-Scale Phenotypic Screening

2019 ◽  
Vol 24 (3) ◽  
pp. 274-283 ◽  
Author(s):  
Vytaute Starkuviene ◽  
Stefan M. Kallenberger ◽  
Nina Beil ◽  
Tautvydas Lisauskas ◽  
Bastian So-Song Schumacher ◽  
...  
Keyword(s):  
New Technologies ◽  
High Density ◽  
Cell Array ◽  
Preclinical Development ◽  
Single Experiment ◽  
Efficient Manner ◽  
Cell Arrays ◽  
High Density Cell ◽  
High Degree ◽  
Genome Scale

Due to high associated costs and considerable time investments of cell-based screening, there is a strong demand for new technologies that enable preclinical development and tests of diverse biologicals in a cost-saving and time-efficient manner. For those reasons we developed the high-density cell array (HD-CA) platform, which miniaturizes cell-based screening in the form of preprinted and ready-to-run screening arrays. With the HD-CA technology, up to 24,576 samples can be tested in a single experiment, thereby saving costs and time for microscopy-based screening by 75%. Experiments on the scale of the entire human genome can be addressed in a real parallel manner, with screening campaigns becoming more comfortable and devoid of robotics infrastructure on the user side. The high degree of miniaturization enables working with expensive reagents and rare and difficult-to-obtain cell lines. We have also optimized an automated imaging procedure for HD-CA and demonstrate the applicability of HD-CA to CRISPR-Cas9- and RNAi-mediated phenotypic assessment of the gene function.

scholarly journals High-throughput subcellular protein localization using cell arrays

2005 ◽  
Vol 33 (6) ◽  
pp. 1407-1408 ◽  
Author(s):  
Y.-H. Hu ◽  
D. Vanhecke ◽  
H. Lehrach ◽  
M. Janitz
Keyword(s):  
High Throughput ◽  
Cellular Localization ◽  
Fluorescent Protein ◽  
Protein Localization ◽  
Open Reading Frames ◽  
Expression Vectors ◽  
Sequence Information ◽  
Cell Array ◽  
Single Experiment ◽  
Cell Arrays

Accomplishment of the human and mouse genome projects resulted in accumulation of extensive gene sequence information. However, the information about the biological functions of the identified genes remains a bottleneck of the post-genomic era. Hence, assays providing simple functional information, such as localization of the protein within the cell, can be very helpful in the elucidation of its function. Transfected cell arrays offer a robust platform for protein localization studies. Open reading frames of unknown genes can be linked to a His6-tag or GFP (green fluorescent protein) reporter in expression vectors and subsequently transfected using the cell array. Cellular localization of the transfected proteins is detected either by specific anti-His-tag antibodies or directly by fluorescence of the GFP fusion protein and by counterstaining with organelle-specific dyes. The high throughput of the method in terms of information provided for every single experiment makes this approach superior to classical immunohistological methods for protein localization.

Planar optical sensors: A tool for screening enzyme activity in high density cell arrays

2006 ◽  
Vol 114 (2) ◽  
pp. 984-994 ◽  
Author(s):  
Jochen Gerlach ◽  
Brigitte Pohn ◽  
Wolfgang Karl ◽  
Marcel Scheideler ◽  
Martina Uray ◽  
...  
Keyword(s):  
Enzyme Activity ◽  
Optical Sensors ◽  
High Density ◽  
Cell Arrays ◽  
High Density Cell

scholarly journals T-SNE visualization of large-scale neural recordings

2016 ◽  
Author(s):  
George Dimitriadis ◽  
Joana Neto ◽  
Adam R. Kampff
Keyword(s):  
Large Scale ◽  
New Technologies ◽  
Dimensional Space ◽  
Clustering Algorithms ◽  
Brain Regions ◽  
Data Sets ◽  
Neural Recordings ◽  
Sorting Problem ◽  
Feature Spaces ◽  
High Degree

AbstractElectrophysiology is entering the era of ‘Big Data’. Multiple probes, each with hundreds to thousands of individual electrodes, are now capable of simultaneously recording from many brain regions. The major challenge confronting these new technologies is transforming the raw data into physiologically meaningful signals, i.e. single unit spikes. Sorting the spike events of individual neurons from a spatiotemporally dense sampling of the extracellular electric field is a problem that has attracted much attention [22, 23], but is still far from solved. Current methods still rely on human input and thus become unfeasible as the size of the data sets grow exponentially.Here we introduce the t-student stochastic neighbor embedding (t-sne) dimensionality reduction method [27] as a visualization tool in the spike sorting process. T-sne embeds the n-dimensional extracellular spikes (n = number of features by which each spike is decomposed) into a low (usually two) dimensional space. We show that such embeddings, even starting from different feature spaces, form obvious clusters of spikes that can be easily visualized and manually delineated with a high degree of precision. We propose that these clusters represent single units and test this assertion by applying our algorithm on labeled data sets both from hybrid [23] and paired juxtacellular/extracellular recordings [15]. We have released a graphical user interface (gui) written in python as a tool for the manual clustering of the t-sne embedded spikes and as a tool for an informed overview and fast manual curration of results from other clustering algorithms. Furthermore, the generated visualizations offer evidence in favor of the use of probes with higher density and smaller electrodes. They also graphically demonstrate the diverse nature of the sorting problem when spikes are recorded with different methods and arise from regions with different background spiking statistics.

Sign in / Sign up

Export Citation Format

Share Document