Literature DB >> 29270442

Low-input Capture-C: A Chromosome Conformation Capture Assay to Analyze Chromatin Architecture in Small Numbers of Cells.

A Marieke Oudelaar1, Damien J Downes1, James O J Davies1, Jim R Hughes1.   

Abstract

Chromosome conformation capture (3C) techniques are crucial to understanding tissue-specific regulation of gene expression, but current methods generally require large numbers of cells. This protocol describes two new low-input Capture-C approaches that can generate high-quality 3C interaction profiles from 10,000-20,000 cells, depending on the resolution used for analysis.

Entities:  

Keywords:  Capture-C; Chromatin architecture; Chromosome conformation capture (3C); Low input; Nuclear organization; Small cell numbers

Year:  2017        PMID： 29270442      PMCID： PMC5736099          DOI： 10.21769/BioProtoc.2645

Source DB:  PubMed          Journal:  Bio Protoc        ISSN： 2331-8325


  5 in total

Review 1.  How best to identify chromosomal interactions: a comparison of approaches.

Authors:  James O J Davies; A Marieke Oudelaar; Douglas R Higgs; Jim R Hughes
Journal:  Nat Methods       Date:  2017-01-31       Impact factor: 28.547

2.  Capturing chromosome conformation.

Authors:  Job Dekker; Karsten Rippe; Martijn Dekker; Nancy Kleckner
Journal:  Science       Date:  2002-02-15       Impact factor: 47.728

3.  Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position.

Authors:  Jason D Buenrostro; Paul G Giresi; Lisa C Zaba; Howard Y Chang; William J Greenleaf
Journal:  Nat Methods       Date:  2013-10-06       Impact factor: 28.547

4.  Robust detection of chromosomal interactions from small numbers of cells using low-input Capture-C.

Authors:  A Marieke Oudelaar; James O J Davies; Damien J Downes; Douglas R Higgs; Jim R Hughes
Journal:  Nucleic Acids Res       Date:  2017-12-15       Impact factor: 16.971

5.  Multiplexed analysis of chromosome conformation at vastly improved sensitivity.

Authors:  James O J Davies; Jelena M Telenius; Simon J McGowan; Nigel A Roberts; Stephen Taylor; Douglas R Higgs; Jim R Hughes
Journal:  Nat Methods       Date:  2015-11-23       Impact factor: 28.547
  5 in total
  4 in total

1.  Robust detection of chromosomal interactions from small numbers of cells using low-input Capture-C.

Authors:  A Marieke Oudelaar; James O J Davies; Damien J Downes; Douglas R Higgs; Jim R Hughes
Journal:  Nucleic Acids Res       Date:  2017-12-15       Impact factor: 16.971

2.  High-resolution targeted 3C interrogation of cis-regulatory element organization at genome-wide scale.

Authors:  Damien J Downes; Robert A Beagrie; Matthew E Gosden; Jelena Telenius; Stephanie J Carpenter; Lea Nussbaum; Sara De Ornellas; Martin Sergeant; Chris Q Eijsbouts; Ron Schwessinger; Jon Kerry; Nigel Roberts; Arun Shivalingam; Afaf El-Sagheer; A Marieke Oudelaar; Tom Brown; Veronica J Buckle; James O J Davies; Jim R Hughes
Journal:  Nat Commun       Date:  2021-01-22       Impact factor: 14.919

3.  Dynamics of the 4D genome during in vivo lineage specification and differentiation.

Authors:  A Marieke Oudelaar; Robert A Beagrie; Matthew Gosden; Sara de Ornellas; Emily Georgiades; Jon Kerry; Daniel Hidalgo; Joana Carrelha; Arun Shivalingam; Afaf H El-Sagheer; Jelena M Telenius; Tom Brown; Veronica J Buckle; Merav Socolovsky; Douglas R Higgs; Jim R Hughes
Journal:  Nat Commun       Date:  2020-06-01       Impact factor: 14.919

4.  A tissue-specific self-interacting chromatin domain forms independently of enhancer-promoter interactions.

Authors:  Jill M Brown; Nigel A Roberts; Bryony Graham; Dominic Waithe; Christoffer Lagerholm; Jelena M Telenius; Sara De Ornellas; A Marieke Oudelaar; Caroline Scott; Izabela Szczerbal; Christian Babbs; Mira T Kassouf; Jim R Hughes; Douglas R Higgs; Veronica J Buckle
Journal:  Nat Commun       Date:  2018-09-21       Impact factor: 14.919
  4 in total

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