Genome-Wide High-Throughput RNAi Screening for Identification of Genes Involved in Protein Production

2018 ◽  
pp. 209-219 ◽  
Author(s):  
Sarah Inwood ◽  
Michael J. Betenbaugh ◽  
Madhu Lal ◽  
Joseph Shiloach
Keyword(s):  
High Throughput ◽  
Protein Production ◽  
Rnai Screening ◽  
Genome Wide

High-Throughput, Liquid-Based Genome-Wide RNAi Screening in C. elegans

2016 ◽  
pp. 151-162 ◽  
Author(s):  
Linda P. O’Reilly ◽  
Ryan R. Knoerdel ◽  
Gary A. Silverman ◽  
Stephen C. Pak
Keyword(s):  
High Throughput ◽  
Rnai Screening ◽  
C Elegans ◽  
Genome Wide

scholarly journals iScreen

2014 ◽  
Vol 20 (8) ◽  
pp. 998-1002 ◽  
Author(s):  
Rui Zhong ◽  
Xiaonan Dong ◽  
Beth Levine ◽  
Yang Xie ◽  
Guanghua Xiao
Keyword(s):  
High Throughput ◽  
R Package ◽  
High Content Screening ◽  
Biological Research ◽  
Analysis Tool ◽  
Rnai Screening ◽  
Genome Wide ◽  
A Genome ◽  
Supplementary Document ◽  
Cellular Phenotypes

High-throughput RNA interference (RNAi) screening has opened up a path to investigating functional genomics in a genome-wide pattern. However, such studies are often restricted to assays that have a single readout format. Recently, advanced image technologies have been coupled with high-throughput RNAi screening to develop high-content screening, in which one or more cell image(s), instead of a single readout, were generated from each well. This image-based high-content screening technology has led to genome-wide functional annotation in a wider spectrum of biological research studies, as well as in drug and target discovery, so that complex cellular phenotypes can be measured in a multiparametric format. Despite these advances, data analysis and visualization tools are still largely lacking for these types of experiments. Therefore, we developed iScreen (image-Based High-content RNAi Screening Analysis Tool), an R package for the statistical modeling and visualization of image-based high-content RNAi screening. Two case studies were used to demonstrate the capability and efficiency of the iScreen package. iScreen is available for download on CRAN ( http://cran.cnr.berkeley.edu/web/packages/iScreen/index.html ). The user manual is also available as a supplementary document.

scholarly journals High-throughput single-cell chromatin accessibility CRISPR screens enable unbiased identification of regulatory networks in cancer

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Sarah E. Pierce ◽  
Jeffrey M. Granja ◽  
William J. Greenleaf
Keyword(s):  
Transcription Factor ◽  
Single Cell ◽  
Cancer Cells ◽  
High Throughput ◽  
Regulatory Networks ◽  
Temporal Dynamics ◽  
Chromatin Accessibility ◽  
Regulatory Regions ◽  
Factor Binding ◽  
Genome Wide

AbstractChromatin accessibility profiling can identify putative regulatory regions genome wide; however, pooled single-cell methods for assessing the effects of regulatory perturbations on accessibility are limited. Here, we report a modified droplet-based single-cell ATAC-seq protocol for perturbing and evaluating dynamic single-cell epigenetic states. This method (Spear-ATAC) enables simultaneous read-out of chromatin accessibility profiles and integrated sgRNA spacer sequences from thousands of individual cells at once. Spear-ATAC profiling of 104,592 cells representing 414 sgRNA knock-down populations reveals the temporal dynamics of epigenetic responses to regulatory perturbations in cancer cells and the associations between transcription factor binding profiles.

scholarly journals A high-throughput genome-wide RNAi screen identifies modifiers of survival motor neuron protein

Cell Reports ◽  
2021 ◽  
Vol 35 (6) ◽  
pp. 109125
Author(s):  
Nikki M. McCormack ◽  
Mahlet B. Abera ◽  
Eveline S. Arnold ◽  
Rebecca M. Gibbs ◽  
Scott E. Martin ◽  
...  
Keyword(s):  
Motor Neuron ◽  
High Throughput ◽  
Rnai Screen ◽  
Survival Motor Neuron ◽  
Survival Motor Neuron Protein ◽  
Genome Wide ◽  
Motor Neuron Protein

scholarly journals Population genetic analysis and phylogeny reconstruction in Eucalyptus (Myrtaceae) using high-throughput, genome-wide genotyping

2011 ◽  
Vol 59 (1) ◽  
pp. 206-224 ◽  
Author(s):  
Dorothy A. Steane ◽  
Dean Nicolle ◽  
Carolina P. Sansaloni ◽  
César D. Petroli ◽  
Jason Carling ◽  
...  
Keyword(s):  
Genetic Analysis ◽  
High Throughput ◽  
Population Genetic ◽  
Phylogeny Reconstruction ◽  
Population Genetic Analysis ◽  
Genome Wide

Genome-wide high throughput analysis of DNA methylation in eukaryotes

Methods ◽  
2009 ◽  
Vol 47 (3) ◽  
pp. 142-150 ◽  
Author(s):  
Kyle R. Pomraning ◽  
Kristina M. Smith ◽  
Michael Freitag
Keyword(s):  
Dna Methylation ◽  
High Throughput ◽  
High Throughput Analysis ◽  
Throughput Analysis ◽  
Genome Wide

scholarly journals Genome-wide C-SWAT library for high-throughput yeast genome tagging

2018 ◽  
Vol 15 (8) ◽  
pp. 598-600 ◽  
Author(s):  
Matthias Meurer ◽  
Yuanqiang Duan ◽  
Ehud Sass ◽  
Ilia Kats ◽  
Konrad Herbst ◽  
...  
Keyword(s):  
High Throughput ◽  
Yeast Genome ◽  
Genome Wide

Comparison of Small- and Large-scale Expression of Selected Pyrococcus furiosus Genes as an Aid to High-throughput Protein Production

2005 ◽  
Vol 6 (2-3) ◽  
pp. 149-158 ◽  
Author(s):  
Frank J. Sugar ◽  
Francis E. Jenney ◽  
Farris L. Poole ◽  
Phillip S. Brereton ◽  
Michi Izumi ◽  
...  
Keyword(s):  
High Throughput ◽  
Large Scale ◽  
Protein Production ◽  
Pyrococcus Furiosus
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