Large-Scale Protein Profiling in Human Cell Lines Using Antibody-Based Proteomics

2011 ◽  
Vol 10 (9) ◽  
pp. 4066-4075 ◽  
Author(s):  
Linn Fagerberg ◽  
Sara Strömberg ◽  
Adila El-Obeid ◽  
Marcus Gry ◽  
Kenneth Nilsson ◽  
...  
Keyword(s):  
Cell Lines ◽  
Human Cell ◽  
Large Scale ◽  
Protein Profiling ◽  
Human Cell Lines

Action of euptox A from Ageratina adenophora juice on human cell lines: A top-down study using FTIR spectroscopy and protein profiling

2019 ◽  
Vol 57 ◽  
pp. 217-225 ◽  
Author(s):  
Rebeca André ◽  
Joana Catarro ◽  
Dalia Freitas ◽  
Rita Pacheco ◽  
M. Conceição Oliveira ◽  
...  
Keyword(s):  
Ftir Spectroscopy ◽  
Cell Lines ◽  
Human Cell ◽  
Protein Profiling ◽  
Human Cell Lines ◽  
Top Down ◽  
Ageratina Adenophora

scholarly journals Large-Scale Population Study of Human Cell Lines Indicates that Dosage Compensation is Virtually Complete

PLoS Genetics ◽  
2005 ◽  
Vol preprint (2007) ◽  
pp. e9
Author(s):  
Colette M Johnston ◽  
Frances L Lovell ◽  
Daniel A Leongamornlert ◽  
Barbara E. Stranger ◽  
Emmanouil T. Dermitzakis ◽  
...  
Keyword(s):  
Cell Lines ◽  
Population Study ◽  
Dosage Compensation ◽  
Human Cell ◽  
Large Scale ◽  
Human Cell Lines ◽  
Scale Population

scholarly journals A scalable strategy for high-throughput GFP tagging of endogenous human proteins

2016 ◽  
Vol 113 (25) ◽  
pp. E3501-E3508 ◽  
Author(s):  
Manuel D. Leonetti ◽  
Sayaka Sekine ◽  
Daichi Kamiyama ◽  
Jonathan S. Weissman ◽  
Bo Huang
Keyword(s):  
Cell Lines ◽  
Human Cell ◽  
Protein Function ◽  
Large Scale ◽  
Protein Complexes ◽  
Protein Localization ◽  
Human Cell Lines ◽  
Guide Rna ◽  
Human Genes ◽  
Endogenous Loci

A central challenge of the postgenomic era is to comprehensively characterize the cellular role of the ∼20,000 proteins encoded in the human genome. To systematically study protein function in a native cellular background, libraries of human cell lines expressing proteins tagged with a functional sequence at their endogenous loci would be very valuable. Here, using electroporation of Cas9 nuclease/single-guide RNA ribonucleoproteins and taking advantage of a split-GFP system, we describe a scalable method for the robust, scarless, and specific tagging of endogenous human genes with GFP. Our approach requires no molecular cloning and allows a large number of cell lines to be processed in parallel. We demonstrate the scalability of our method by targeting 48 human genes and show that the resulting GFP fluorescence correlates with protein expression levels. We next present how our protocols can be easily adapted for the tagging of a given target with GFP repeats, critically enabling the study of low-abundance proteins. Finally, we show that our GFP tagging approach allows the biochemical isolation of native protein complexes for proteomic studies. Taken together, our results pave the way for the large-scale generation of endogenously tagged human cell lines for the proteome-wide analysis of protein localization and interaction networks in a native cellular context.

scholarly journals iCSDB: an integrated database of CRISPR screens

2020 ◽  
Vol 49 (D1) ◽  
pp. D956-D961
Author(s):  
Ahyoung Choi ◽  
Insu Jang ◽  
Heewon Han ◽  
Min-Seo Kim ◽  
Jinhyuk Choi ◽  
...  
Keyword(s):  
Cell Lines ◽  
Human Cell ◽  
High Throughput Screening ◽  
Large Scale ◽  
Target Genes ◽  
Human Cell Lines ◽  
Guide Rna ◽  
Functional Studies ◽  
Screening Experiments ◽  
Public Data

Abstract High-throughput screening based on CRISPR-Cas9 libraries has become an attractive and powerful technique to identify target genes for functional studies. However, accessibility of public data is limited due to the lack of user-friendly utilities and up-to-date resources covering experiments from third parties. Here, we describe iCSDB, an integrated database of CRISPR screening experiments using human cell lines. We compiled two major sources of CRISPR-Cas9 screening: the DepMap portal and BioGRID ORCS. DepMap portal itself is an integrated database that includes three large-scale projects of CRISPR screening. We additionally aggregated CRISPR screens from BioGRID ORCS that is a collection of screening results from PubMed articles. Currently, iCSDB contains 1375 genome-wide screens across 976 human cell lines, covering 28 tissues and 70 cancer types. Importantly, the batch effects from different CRISPR libraries were removed and the screening scores were converted into a single metric to estimate the knockout efficiency. Clinical and molecular information were also integrated to help users to select cell lines of interest readily. Furthermore, we have implemented various interactive tools and viewers to facilitate users to choose, examine and compare the screen results both at the gene and guide RNA levels. iCSDB is available at https://www.kobic.re.kr/icsdb/.

scholarly journals Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing

2018 ◽  
Author(s):  
Isac Lee ◽  
Roham Razaghi ◽  
Timothy Gilpatrick ◽  
Michael Molnar ◽  
Norah Sadowski ◽  
...  
Keyword(s):  
Cell Lines ◽  
Human Cell ◽  
Large Scale ◽  
Human Cancer ◽  
Chromatin Accessibility ◽  
Nanopore Sequencing ◽  
Human Cell Lines ◽  
Sequencing Data ◽  
Structural Variations ◽  
Genetic Changes

ABSTRACTUnderstanding how the genome and the epigenome work together to control gene transcription has applications in our understanding of diseases such as human cancer. In this study, we combine the ability of NOMe-seq to simultaneously evaluate CpG methylation and chromatin accessibility, with long-read nanopore sequencing technology, a method we call nanoNOMe. We generated >60Gb whole-genome nanopore sequencing data for each of four human cell lines (GM12878, MCF-10A, MCF-7, MDA-MB-231) including repetitive regions inaccessible by short read sequencing. Using the long reads, we find that we can observe phased methylation and chromatin accessibility, large scale pattern changes, and genetic changes such as structural variations from a single assay.

scholarly journals A scalable strategy for high-throughput GFP tagging of endogenous human proteins

2016 ◽  
Author(s):  
Manuel D. Leonetti ◽  
Sayaka Sekine ◽  
Daichi Kamiyama ◽  
Jonathan S. Weissman ◽  
Bo Huang
Keyword(s):  
Cell Lines ◽  
Human Cell ◽  
Large Scale ◽  
Human Proteome ◽  
Human Cell Lines ◽  
Functional Sequence ◽  
Human Genes ◽  
Human Proteins ◽  
The Way

AbstractA central challenge of the post-genomic era is to comprehensively characterize the cellular role of the ∼20,000 proteins encoded in the human genome. To systematically study protein function in a native cellular background, libraries of human cell lines expressing proteins tagged with a functional sequence at their endogenous loci would be very valuable. Here, using electroporation of Cas9/sgRNA ribonucleoproteins and taking advantage of a split-GFP system, we describe a scalable method for the robust, scarless and specific tagging of endogenous human genes with GFP. Our approach requires no molecular cloning and allows a large number of cell lines to be processed in parallel. We demonstrate the scalability of our method by targeting 48 human genes and show that the resulting GFP fluorescence correlates with protein expression levels. We next present how our protocols can be easily adapted for the tagging of a given target with GFP repeats, critically enabling the study of low-abundance proteins. Finally, we show that our GFP tagging approach allows the biochemical isolation of native protein complexes for proteomic studies. Together, our results pave the way for the large-scale generation of endogenously tagged human cell lines for the proteome-wide analysis of protein localization and interaction networks in a native cellular context.SIGNIFICANCE STATEMENTThe function of a large fraction of the human proteome still remains poorly characterized. Tagging proteins with a functional sequence is a powerful way to access function, and inserting tags at endogenous genomic loci allows the preservation of a near-native cellular background. To characterize the cellular role of human proteins in a systematic manner and in a native context, we developed a method for tagging endogenous human proteins with GFP that is both rapid and readily applicable at a genome-wide scale. Our approach allows studying both localization and interaction partners of the protein target. Our results pave the way for the large-scale generation of endogenously tagged human cell lines for a systematic functional interrogation of the human proteome.

scholarly journals Large-Scale Population Study of Human Cell Lines Indicates that Dosage Compensation Is Virtually Complete

PLoS Genetics ◽  
2008 ◽  
Vol 4 (1) ◽  
pp. e9 ◽  
Author(s):  
Colette M Johnston ◽  
Frances L Lovell ◽  
Daniel A Leongamornlert ◽  
Barbara E Stranger ◽  
Emmanouil T Dermitzakis ◽  
...  
Keyword(s):  
Cell Lines ◽  
Population Study ◽  
Dosage Compensation ◽  
Human Cell ◽  
Large Scale ◽  
Human Cell Lines ◽  
Scale Population

Investigations of the influence of microgravity on the state of human cell lines

2004 ◽  
Vol 10 (5-6) ◽  
pp. 226-228
Author(s):  
L.M. Nosach ◽  
◽  
O.Yu. Povnitsa ◽  
V.L. Zhovnovata ◽  
◽  
...  
Keyword(s):  
Cell Lines ◽  
Human Cell ◽  
The State ◽  
Human Cell Lines
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