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Aire controls gene expression in the thymic epithelium with ordered stochasticity
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scholarly article
1 reference
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Europe PubMed Central
PMCID
4632529
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26237550%20AND%20SRC:MED&resulttype=core&format=json
retrieved
20 February 2020
title
Aire controls gene expression in the thymic epithelium with ordered stochasticity
(English)
1 reference
stated in
Europe PubMed Central
PMCID
4632529
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26237550%20AND%20SRC:MED&resulttype=core&format=json
retrieved
20 February 2020
main subject
RNA sequencing
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single cell transcriptomics
1 reference
stated in
A curated database reveals trends in single-cell transcriptomics
reference URL
https://www.nxn.se/single-cell-studies/data.tsv
retrieved
7 February 2021
author
David Zemmour
series ordinal
2
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Europe PubMed Central
PMCID
4632529
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26237550%20AND%20SRC:MED&resulttype=core&format=json
retrieved
20 February 2020
author name string
Matthew Meredith
series ordinal
1
1 reference
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Europe PubMed Central
PMCID
4632529
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26237550%20AND%20SRC:MED&resulttype=core&format=json
retrieved
20 February 2020
Diane Mathis
series ordinal
3
1 reference
stated in
Europe PubMed Central
PMCID
4632529
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26237550%20AND%20SRC:MED&resulttype=core&format=json
retrieved
20 February 2020
Christophe Benoist
series ordinal
4
1 reference
stated in
Europe PubMed Central
PMCID
4632529
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26237550%20AND%20SRC:MED&resulttype=core&format=json
retrieved
20 February 2020
language of work or name
English
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publication date
3 August 2015
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stated in
Europe PubMed Central
PMCID
4632529
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26237550%20AND%20SRC:MED&resulttype=core&format=json
retrieved
20 February 2020
external data available at URL
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70798
1 reference
stated in
A curated database reveals trends in single-cell transcriptomics
reference URL
https://www.nxn.se/single-cell-studies/data.tsv
retrieved
7 February 2021
published in
Nature Immunology
1 reference
stated in
Europe PubMed Central
PMCID
4632529
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26237550%20AND%20SRC:MED&resulttype=core&format=json
retrieved
20 February 2020
volume
16
1 reference
stated in
Europe PubMed Central
PMCID
4632529
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26237550%20AND%20SRC:MED&resulttype=core&format=json
retrieved
20 February 2020
issue
9
1 reference
stated in
Europe PubMed Central
PMCID
4632529
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26237550%20AND%20SRC:MED&resulttype=core&format=json
retrieved
20 February 2020
page(s)
942-949
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Europe PubMed Central
PMCID
4632529
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26237550%20AND%20SRC:MED&resulttype=core&format=json
retrieved
20 February 2020
describes a project that uses
CEL-seq
1 reference
stated in
A curated database reveals trends in single-cell transcriptomics
reference URL
https://www.nxn.se/single-cell-studies/data.tsv
retrieved
7 February 2021
cites work
Population and single-cell genomics reveal the Aire dependency, relief from Polycomb silencing, and distribution of self-antigen expression in thymic epithelia
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PubMed Central
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The transcriptional regulator Aire coopts the repressive ATF7ip-MBD1 complex for the induction of immunotolerance.
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An RNAi screen for Aire cofactors reveals a role for Hnrnpl in polymerase release and Aire-activated ectopic transcription
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1 October 2017
Overlapping gene coexpression patterns in human medullary thymic epithelial cells generate self-antigen diversity
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Single-cell sequencing-based technologies will revolutionize whole-organism science
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1 October 2017
Aire-dependent thymic development of tumor-associated regulatory T cells
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632529
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1 October 2017
AIRE-PHD fingers are structural hubs to maintain the integrity of chromatin-associated interactome
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632529
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CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification
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PubMed Central
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1 October 2017
Aire unleashes stalled RNA polymerase to induce ectopic gene expression in thymic epithelial cells
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632529
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1 October 2017
Gene bookmarking accelerates the kinetics of post-mitotic transcriptional re-activation
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1 October 2017
APCluster: an R package for affinity propagation clustering
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632529
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1 October 2017
Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632529
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1 October 2017
Aire's partners in the molecular control of immunological tolerance
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stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632529
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1 October 2017
AIRE activated tissue specific genes have histone modifications associated with inactive chromatin
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632529
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1 October 2017
Regulated fluctuations in nanog expression mediate cell fate decisions in embryonic stem cells
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632529
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1 October 2017
The impact of negative selection on thymocyte migration in the medulla.
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632529
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1 October 2017
Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632529
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1 October 2017
Transcriptional regulation by AIRE: molecular mechanisms of central tolerance
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632529
retrieved
1 October 2017
Aire employs a histone-binding module to mediate immunological tolerance, linking chromatin regulation with organ-specific autoimmunity.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632529
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1 October 2017
The variable immunological self: genetic variation and nongenetic noise in Aire-regulated transcription
1 reference
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PubMed Central
reference URL
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1 October 2017
Ectopic expression of peripheral-tissue antigens in the thymic epithelium: probabilistic, monoallelic, misinitiated
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632529
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1 October 2017
Deletional tolerance mediated by extrathymic Aire-expressing cells
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632529
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1 October 2017
The autoimmune regulator PHD finger binds to non-methylated histone H3K4 to activate gene expression
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632529
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1 October 2017
Promiscuous gene expression patterns in single medullary thymic epithelial cells argue for a stochastic mechanism
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632529
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1 October 2017
AIRE recruits multiple transcriptional components to specific genomic regions through tethering to nuclear matrix
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632529
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1 October 2017
Promiscuous gene expression in thymic epithelial cells is regulated at multiple levels
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632529
retrieved
1 October 2017
Chromosomal clustering of genes controlled by the aire transcription factor
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632529
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1 October 2017
Control of stochasticity in eukaryotic gene expression
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632529
retrieved
1 October 2017
Aire regulates negative selection of organ-specific T cells
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632529
retrieved
1 October 2017
Projection of an immunological self shadow within the thymus by the aire protein
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632529
retrieved
1 October 2017
Stochastic gene expression in a single cell
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632529
retrieved
1 October 2017
Regulation of noise in the expression of a single gene
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632529
retrieved
1 October 2017
Large-scale analysis of the human and mouse transcriptomes
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632529
retrieved
1 October 2017
High frequency of autoreactive myelin proteolipid protein-specific T cells in the periphery of naive mice: mechanisms of selection of the self-reactive repertoire
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632529
retrieved
1 October 2017
Evidence for a single-niche model of positive selection
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632529
retrieved
1 October 2017
Promiscuous mRNA splicing under the control of AIRE in medullary thymic epithelial cells.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632529
retrieved
29 June 2018
The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632529
retrieved
29 June 2018
Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications.
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632529
retrieved
29 June 2018
AIRE recruits P-TEFb for transcriptional elongation of target genes in medullary thymic epithelial cells
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632529
retrieved
29 June 2018
Transcription of individual genes in eukaryotic cells occurs randomly and infrequently
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632529
retrieved
29 June 2018
Aire regulates the transfer of antigen from mTECs to dendritic cells for induction of thymic tolerance.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632529
retrieved
22 September 2018
Highly variable expression of tissue-restricted self-antigens in human thymus: implications for self-tolerance and autoimmunity.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632529
retrieved
22 September 2018
The cellular mechanism of Aire control of T cell tolerance.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632529
retrieved
22 September 2018
Shaping of the autoreactive T-cell repertoire by a splice variant of self protein expressed in thymic epithelial cells.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632529
retrieved
22 September 2018
The autoimmune regulator PHD finger binds to non-methylated histone H3K4 to activate gene expression
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632529
retrieved
5 December 2018
Generation of a complete thymic microenvironment by MTS24(+) thymic epithelial cells
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/26237550
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
Identifiers
DOI
10.1038/NI.3247
1 reference
stated in
Europe PubMed Central
PMCID
4632529
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26237550%20AND%20SRC:MED&resulttype=core&format=json
retrieved
20 February 2020
PMCID
4632529
1 reference
stated in
Europe PubMed Central
PMCID
4632529
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26237550%20AND%20SRC:MED&resulttype=core&format=json
retrieved
20 February 2020
PubMed ID
26237550
1 reference
stated in
Europe PubMed Central
PMCID
4632529
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26237550%20AND%20SRC:MED&resulttype=core&format=json
retrieved
20 February 2020
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