ChIP-seq and RNA-seq methods to study circadian control of transcription in mammals (Q35557825)

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29 February 2020

title

ChIP-seq and RNA-seq methods to study circadian control of transcription in mammals (English)

1 reference

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29 February 2020

0 references

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1

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29 February 2020

author name string

Vivek Kumar

2

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29 February 2020

Prachi Nakashe

3

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29 February 2020

Nobuya Koike

4

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29 February 2020

Hung-Chung Huang

5

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29 February 2020

Carla B Green

6

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29 February 2020

Tae-Kyung Kim

7

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29 February 2020

language of work or name

English

0 references

publication date

26 December 2014

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29 February 2020

published in

Methods in Enzymology

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29 February 2020

volume

551

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29 February 2020

page(s)

285-321

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TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

29 February 2020

cites work

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Circadian oscillations of protein-coding and regulatory RNAs in a highly dynamic mammalian liver epigenome

12 July 2018

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Genome-wide RNA polymerase II profiles and RNA accumulation reveal kinetics of transcription and associated epigenetic changes during diurnal cycles

12 July 2018

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Nascent-Seq reveals novel features of mouse circadian transcriptional regulation

12 July 2018

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Transcriptional architecture and chromatin landscape of the core circadian clock in mammals

12 July 2018

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Fast gapped-read alignment with Bowtie 2

12 July 2018

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Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain

12 July 2018

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Genetics of circadian rhythms in Mammalian model organisms

12 July 2018

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Genome-wide and phase-specific DNA-binding rhythms of BMAL1 control circadian output functions in mouse liver

12 July 2018

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Genome-wide profiling of the core clock protein BMAL1 targets reveals a strict relationship with metabolism

12 July 2018

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JTK_CYCLE: an efficient nonparametric algorithm for detecting rhythmic components in genome-scale data sets

12 July 2018

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PeakAnalyzer: genome-wide annotation of chromatin binding and modification loci.

12 July 2018

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Analyzing circadian expression data by harmonic regression based on autoregressive spectral estimation

12 July 2018

1 reference

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Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities

12 July 2018

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c-Myc regulates transcriptional pause release

12 July 2018

1 reference

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Rhythmic PER abundance defines a critical nodal point for negative feedback within the circadian clock mechanism

12 July 2018

1 reference

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The Sequence Alignment/Map format and SAMtools

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402199

Model-based analysis of ChIP-Seq (MACS)

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402199

Transcribing RNA polymerase II is phosphorylated at CTD residue serine-7.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402199

Two-step cross-linking method for identification of NF-kappaB gene network by chromatin immunoprecipitation.

12 July 2018

1 reference

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Mammalian circadian biology: elucidating genome-wide levels of temporal organization

12 July 2018

1 reference

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C-terminal repeat domain kinase I phosphorylates Ser2 and Ser5 of RNA polymerase II C-terminal domain repeats

12 July 2018

1 reference

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ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments

12 July 2018

1 reference

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Direct association between mouse PERIOD and CKIepsilon is critical for a functioning circadian clock

12 July 2018

1 reference

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Coordinated transcription of key pathways in the mouse by the circadian clock

12 July 2018

1 reference

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Posttranslational mechanisms regulate the mammalian circadian clock

12 July 2018

1 reference

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NPAS2: an analog of clock operative in the mammalian forebrain

12 July 2018

1 reference

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Mop3 is an essential component of the master circadian pacemaker in mammals

12 July 2018

1 reference

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Genome-wide location and function of DNA binding proteins

12 July 2018

1 reference

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In vivo cross-linking and immunoprecipitation for studying dynamic Protein:DNA associations in a chromatin environment

12 July 2018

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mCRY1 and mCRY2 are essential components of the negative limb of the circadian clock feedback loop

12 July 2018

1 reference

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Role of the CLOCK protein in the mammalian circadian mechanism

12 July 2018

1 reference

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Positional cloning of the mouse circadian clock gene

12 July 2018

1 reference

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Association of p300 and CBP with simian virus 40 large T antigen

12 July 2018

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Role of the suprachiasmatic nuclei in the circadian system of the house sparrow, Passer domesticus

12 July 2018

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Detecting protein-DNA interactions in vivo: distribution of RNA polymerase on specific bacterial genes

12 July 2018

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Formaldehyde-mediated DNA-protein crosslinking: a probe for in vivo chromatin structures

12 July 2018

1 reference

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Studies on histone organization in the nucleosome using formaldehyde as a reversible cross-linking agent

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402199

Formaldehyde as a probe of DNA structure. II. Reaction with endocyclic imino groups of DNA bases

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402199

Formaldehyde as a probe of DNA structure. I. Reaction with exocyclic amino groups of DNA bases

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402199

In vivo dual cross-linking for identification of indirect DNA-associated proteins by chromatin immunoprecipitation

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402199

Isolation and identification of cross-links from formaldehyde-treated nucleic acids

26 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25662462

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

A new method for the isolation of replicative chromatin: selective deposition of histone on both new and old DNA

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25662462

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Chromatin structure of hsp 70 genes, activated by heat shock: selective removal of histones from the coding region and their absence from the 5' region

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25662462

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1016/BS.MIE.2014.10.059

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25662462%20AND%20SRC:MED&resulttype=core&format=json

29 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25662462%20AND%20SRC:MED&resulttype=core&format=json

29 February 2020

PubMed publication ID

25662462

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25662462%20AND%20SRC:MED&resulttype=core&format=json