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Plant Gene Regulatory Networks

Overview of attention for book
Cover of 'Plant Gene Regulatory Networks'

Table of Contents

  1. Altmetric Badge
    Book Overview
  2. Altmetric Badge
    Chapter 1 From Genes to Networks: Characterizing Gene-Regulatory Interactions in Plants
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    Chapter 2 Inducible Promoter Systems for Gene Perturbation Experiments in Arabidopsis
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    Chapter 3 Cell Type-Specific Gene Expression Profiling Using Fluorescence-Activated Nuclear Sorting
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    Chapter 4 Characterization of Cell-Type-Specific DNA Binding Sites of Plant Transcription Factors Using Chromatin Immunoprecipitation
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    Chapter 5 Yeast One- and Two-Hybrid High-Throughput Screenings Using Arrayed Libraries
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    Chapter 6 SELEX-Seq: A Method to Determine DNA Binding Specificities of Plant Transcription Factors
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    Chapter 7 Analysis of a Plant Transcriptional Regulatory Network Using Transient Expression Systems
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    Chapter 8 Analysis of In Vivo Chromatin and Protein Interactions of Arabidopsis Transcript Elongation Factors
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    Chapter 9 Characterization of Mediator Complex and its Associated Proteins from Rice
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    Chapter 10 DNase I SIM: A Simplified In-Nucleus Method for DNase I Hypersensitive Site Sequencing
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    Chapter 11 In Situ Hi-C Library Preparation for Plants to Study Their Three-Dimensional Chromatin Interactions on a Genome-Wide Scale
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    Chapter 12 Multiplexed Transcriptional Activation or Repression in Plants Using CRISPR-dCas9-Based Systems
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    Chapter 13 Generation of dTALEs and Libraries of Synthetic TALE-Activated Promoters for Engineering of Gene Regulatory Networks in Plants
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    Chapter 14 Design of Knowledge Bases for Plant Gene Regulatory Networks
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    Chapter 15 AraNet: A Network Biology Server for Arabidopsis thaliana and Other Non-Model Plant Species
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    Chapter 16 Integration of Genome-Wide TF Binding and Gene Expression Data to Characterize Gene Regulatory Networks in Plant Development
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    Chapter 17 Predicting Transcription Factor Binding Sites and Their Cognate Transcription Factors Using Gene Expression Data
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    Chapter 18 Computational Approaches to Study Gene Regulatory Networks
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    Chapter 19 Boolean Dynamic Modeling Approaches to Study Plant Gene Regulatory Networks: Integration, Validation, and Prediction
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    Chapter 20 ODE-Based Modeling of Complex Regulatory Circuits
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    Chapter 21 Inferring Gene Regulatory Networks in the Arabidopsis Root Using a Dynamic Bayesian Network Approach
Attention for Chapter 11: In Situ Hi-C Library Preparation for Plants to Study Their Three-Dimensional Chromatin Interactions on a Genome-Wide Scale
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Chapter title
In Situ Hi-C Library Preparation for Plants to Study Their Three-Dimensional Chromatin Interactions on a Genome-Wide Scale
Chapter number 11
Book title
Plant Gene Regulatory Networks
Published in
Methods in molecular biology, June 2017
DOI 10.1007/978-1-4939-7125-1_11
Pubmed ID
28623585
Book ISBNs
978-1-4939-7124-4, 978-1-4939-7125-1
Authors

Chang Liu

Editors

Kerstin Kaufmann, Bernd Mueller-Roeber

Abstract

The spatial organization of the genome in the nucleus is critical for many cellular processes. It has been broadly accepted that the packing of chromatin inside the nucleus is not random, but structured at several hierarchical levels. The Hi-C method combines Chromatin Conformation Capture and high-throughput sequencing, which allows interrogating genome-wide chromatin interactions. Depending on the sequencing depth, chromatin packing patterns derived from Hi-C experiments can be viewed on a chromosomal scale or at a local genic level. Here, I describe a protocol of plant in situ Hi-C library preparation, which covers procedures starting from tissue fixation to library amplification.

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X Demographics

X Demographics

The data shown below were collected from the profile of 1 X user who shared this research output. Click here to find out more about how the information was compiled.
 Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 29 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 29 100%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 10 34%
Researcher 5 17%
Student > Bachelor 3 10%
Professor 1 3%
Other 1 3%
Other 2 7%
Unknown 7 24%
Readers by discipline Count As %
Agricultural and Biological Sciences 9 31%
Biochemistry, Genetics and Molecular Biology 9 31%
Environmental Science 2 7%
Immunology and Microbiology 2 7%
Chemistry 1 3%
Other 0 0%
Unknown 6 21%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 14 March 2018.
All research outputs
#15,469,838
of 22,988,380 outputs
Outputs from Methods in molecular biology
#5,380
of 13,149 outputs
Outputs of similar age
#198,947
of 316,939 outputs
Outputs of similar age from Methods in molecular biology
#97
of 280 outputs
Altmetric has tracked 22,988,380 research outputs across all sources so far. This one is in the 22nd percentile – i.e., 22% of other outputs scored the same or lower than it.
So far Altmetric has tracked 13,149 research outputs from this source. They receive a mean Attention Score of 3.4. This one is in the 44th percentile – i.e., 44% of its peers scored the same or lower than it.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 316,939 tracked outputs that were published within six weeks on either side of this one in any source. This one is in the 28th percentile – i.e., 28% of its contemporaries scored the same or lower than it.
We're also able to compare this research output to 280 others from the same source and published within six weeks on either side of this one. This one is in the 47th percentile – i.e., 47% of its contemporaries scored the same or lower than it.

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