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001-es BibID:BIBFORM100565
035-os BibID:(cikkazonosító)52150
Első szerző:Berguet, Geoffrey
Cím:Automating ChIP-seq Experiments to Generate Epigenetic Profiles on 10,000 HeLa Cells / Geoffrey Berguet, Jan Hendrickx, Celine Sabatel, Miklos Laczik, Sharon Squazzo, Ignacio Mazon Pelaez, Rini Saxena, Helene Pendeville, Dominique Poncelet
Dátum:2014
ISSN:1940-087X
Megjegyzések:Chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq) is a technique of choice for studying protein-DNA interactions. ChIP-seq has been used for mapping protein-DNA interactions and allocating histones modifications. The procedure is tedious and time consuming, and one of the major limitations is the requirement for high amounts of starting material, usually millions of cells. Automation of chromatin immunoprecipitation assays is possible when the procedure is based on the use of magnetic beads. Successful automated protocols of chromatin immunoprecipitation and library preparation have been specifically designed on a commercially available robotic liquid handling system dedicated mainly to automate epigenetic assays. First, validation of automated ChIP-seq assays using antibodies directed against various histone modifications was shown, followed by optimization of the automated protocols to perform chromatin immunoprecipitation and library preparation starting with low cell numbers. The goal of these experiments is to provide a valuable tool for future epigenetic analysis of specific cell types, sub-populations, and biopsy samples.
Tárgyszavak:Természettudományok Biológiai tudományok idegen nyelvű folyóiratközlemény külföldi lapban
folyóiratcikk
Megjelenés:Journal of Visualized Experiments. - 2014 : 94 (2014), p. 1-11. -
További szerzők:Hendrickx, Jan Sabatel, Celine Laczik Miklós (1985-) (bioinformatikus/molekuláris biológus) Squazzo, Sharon Mazon Pelaez, Ignacio Saxena, Rini Pendeville, Helene Poncelet, Dominique
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001-es BibID:BIBFORM100563
Első szerző:Laczik Miklós (bioinformatikus/molekuláris biológus)
Cím:Iterative Fragmentation Improves the Detection of ChIP-seq Peaks for Inactive Histone Marks / Miklós Laczik, Jan Hendrickx, Anne-Clémence Veillard, Mustafa Tammoh, Sarah Marzi, Dominique Poncelet
Dátum:2016
ISSN:1177-9322
Megjegyzések:As chromatin immunoprecipitation (ChIP) sequencing is becoming the dominant technique for studying chromatin modifications, new protocols surface to improve the method. Bioinformatics is also essential to analyze and understand the results, and precise analysis helps us to identify the effects of protocol optimizations. We applied iterative sonication ? sending the fragmented DNA after ChIP through additional round(s) of shearing ? to a number of samples, testing the effects on different histone marks, aiming to uncover potential benefits of inactive histone marks specifically. We developed an analysis pipeline that utilizes our unique, enrichment-type specific approach to peak calling. With the help of this pipeline, we managed to accurately describe the advantages and disadvantages of the iterative refragmentation technique, and we successfully identified possible fields for its applications, where it enhances the results greatly. In addition to the resonication protocol description, we provide guidelines for peak calling optimization and a freely implementable pipeline for data analysis.
Tárgyszavak:Orvostudományok Elméleti orvostudományok idegen nyelvű folyóiratközlemény külföldi lapban
folyóiratcikk
Megjelenés:Bioinformatics and Biology Insights. - 10 (2016), p. 209-224. -
További szerzők:Hendrickx, Jan Veillard, Anne-Clémence Tammoh, Mustafa Marzi, Sarah Poncelet, Dominique
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DOI
Intézményi repozitóriumban (DEA) tárolt változat
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