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EndoC-βH1 multi-genomic profiling defines gene regulatory programs governing human pancreatic β cell identity and function

https://doi.org/10.1101/399139
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Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/hep.24590openalex-snapshot
Multipotent stem/progenitor cells in human biliary tree give rise to hepatocytes, cholangiocytes, and pancreatic islets
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Differential Oestrogen Receptor Binding is Associated with Clinical Outcome in Breast Cancer
inferredcites →https://doi.org/10.1007/s00125-011-2283-5openalex-snapshot
Transcriptomes of the major human pancreatic cell types
inferredcites →https://doi.org/10.1007/s00125-016-4060-yopenalex-snapshot
Sensitivity profile of the human EndoC-βH1 beta cell line to proinflammatory cytokines
inferredcites →https://doi.org/10.1007/s11892-011-0224-9openalex-snapshot
Gene × Environment Interactions in Type 2 Diabetes
inferredcites →https://doi.org/10.1016/b978-0-12-407190-2.00001-0openalex-snapshot
Understanding the Role of ETS-Mediated Gene Regulation in Complex Biological Processes
inferredcites →https://doi.org/10.1016/j.ajhg.2012.08.002openalex-snapshot
Genetic Risk Factors for Type 2 Diabetes: A Trans-Regulatory Genetic Architecture?
inferredcites →https://doi.org/10.1016/j.bbrc.2015.05.072openalex-snapshot
Physiological characterization of the human EndoC-βH1 β-cell line
inferredcites →https://doi.org/10.1016/j.cell.2014.11.021openalex-snapshot
A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
inferredcites →https://doi.org/10.1016/j.celrep.2015.02.004openalex-snapshot
Comparative Hi-C Reveals that CTCF Underlies Evolution of Chromosomal Domain Architecture
inferredcites →https://doi.org/10.1016/j.cels.2015.07.012openalex-snapshot
Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom
inferredcites →https://doi.org/10.1016/j.cels.2015.08.001openalex-snapshot
Transcription Factor Competition Allows Embryonic Stem Cells to Distinguish Authentic Signals from Noise
inferredcites →https://doi.org/10.1016/j.cels.2016.07.002openalex-snapshot
Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments
inferredcites →https://doi.org/10.1016/j.cels.2016.08.011openalex-snapshot
A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure
inferredcites →https://doi.org/10.1016/j.cels.2016.09.002openalex-snapshot
A Single-Cell Transcriptome Atlas of the Human Pancreas
inferredcites →https://doi.org/10.1016/j.cmet.2010.09.012openalex-snapshot
Global Epigenomic Analysis of Primary Human Pancreatic Islets Provides Insights into Type 2 Diabetes Susceptibility Loci
inferredcites →https://doi.org/10.1016/j.cmet.2014.03.001openalex-snapshot
The Complement Inhibitor CD59 Regulates Insulin Secretion by Modulating Exocytotic Events
inferredcites →https://doi.org/10.1016/j.cmet.2016.08.018openalex-snapshot
RNA Sequencing of Single Human Islet Cells Reveals Type 2 Diabetes Genes
inferredcites →https://doi.org/10.1016/j.cmet.2016.08.020openalex-snapshot
Single-Cell Transcriptome Profiling of Human Pancreatic Islets in Health and Type 2 Diabetes
inferredcites →https://doi.org/10.1016/j.mce.2017.02.043openalex-snapshot
The small RNA miR-375 – a pancreatic islet abundant miRNA with multiple roles in endocrine beta cell function
inferredcites →https://doi.org/10.1016/j.mod.2009.09.006openalex-snapshot
Multiple, temporal-specific roles for HNF6 in pancreatic endocrine and ductal differentiation
inferredcites →https://doi.org/10.1016/j.molcel.2010.05.004openalex-snapshot
Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities
inferredcites →https://doi.org/10.1016/j.molmet.2016.01.002openalex-snapshot
Integration of ATAC-seq and RNA-seq identifies human alpha cell and beta cell signature genes
inferredcites →https://doi.org/10.1016/j.molmet.2017.03.011openalex-snapshot
Expression and functional assessment of candidate type 2 diabetes susceptibility genes identify four new genes contributing to human insulin secretion
inferredcites →https://doi.org/10.1016/j.molmet.2017.12.007openalex-snapshot
The EndoC-βH1 cell line is a valid model of human beta cells and applicable for screenings to identify novel drug target candidates
inferredcites →https://doi.org/10.1016/j.tig.2017.01.010openalex-snapshot
Genomics of Islet (Dys)function and Type 2 Diabetes
inferredcites →https://doi.org/10.1016/j.ydbio.2006.02.028openalex-snapshot
A switch from MafB to MafA expression accompanies differentiation to pancreatic β-cells
inferredcites →https://doi.org/10.1016/j.ymeth.2012.05.001openalex-snapshot
Hi–C: A comprehensive technique to capture the conformation of genomes
inferredcites →https://doi.org/10.1016/s1074-7613(01)00085-1openalex-snapshot
NFATc1 and NFATc2 Together Control Both T and B Cell Activation and Differentiation
inferredcites →https://doi.org/10.1038/emboj.2011.503openalex-snapshot
DNA methylation profiling identifies epigenetic dysregulation in pancreatic islets from type 2 diabetic patients
inferredcites →https://doi.org/10.1038/msb.2011.54openalex-snapshot
AlleleSeq: analysis of allele‐specific expression and binding in a network framework
inferredcites →https://doi.org/10.1038/nature10730openalex-snapshot
Differential oestrogen receptor binding is associated with clinical outcome in breast cancer
inferredcites →https://doi.org/10.1038/nature11247openalex-snapshot
An integrated encyclopedia of DNA elements in the human genome
inferredcites →https://doi.org/10.1038/nature14248openalex-snapshot
Integrative analysis of 111 reference human epigenomes
inferredcites →https://doi.org/10.1038/nature14465openalex-snapshot
Human body epigenome maps reveal noncanonical DNA methylation variation
inferredcites →https://doi.org/10.1038/nature18642openalex-snapshot
The genetic architecture of type 2 diabetes
inferredcites →https://doi.org/10.1038/nbt.1630openalex-snapshot
GREAT improves functional interpretation of cis-regulatory regions
inferredcites →https://doi.org/10.1038/ncomms11764openalex-snapshot
The genetic regulatory signature of type 2 diabetes in human skeletal muscle
inferredcites →https://doi.org/10.1038/ng.2870openalex-snapshot
Pancreatic islet enhancer clusters enriched in type 2 diabetes risk-associated variants
inferredcites →https://doi.org/10.1038/ng.2897openalex-snapshot
Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility
inferredcites →https://doi.org/10.1038/ng.3437openalex-snapshot
Genetic fine mapping and genomic annotation defines causal mechanisms at type 2 diabetes susceptibility loci
inferredcites →https://doi.org/10.1038/ng.3571openalex-snapshot
Fast and accurate long-range phasing in a UK Biobank cohort
inferredcites →https://doi.org/10.1038/ng.3643openalex-snapshot
A reference panel of 64,976 haplotypes for genotype imputation
inferredcites →https://doi.org/10.1038/ng.3656openalex-snapshot
Next-generation genotype imputation service and methods
inferredcites →https://doi.org/10.1038/nmeth.1785openalex-snapshot
A linear complexity phasing method for thousands of genomes
inferredcites →https://doi.org/10.1038/nmeth.2688openalex-snapshot
Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position
inferredcites →https://doi.org/10.1038/nmeth.3582openalex-snapshot
WASP: allele-specific software for robust molecular quantitative trait locus discovery
inferredcites →https://doi.org/10.1038/nprot.2017.012openalex-snapshot
Long-read ChIA-PET for base-pair-resolution mapping of haplotype-specific chromatin interactions
inferredcites →https://doi.org/10.1038/nprot.2017.124openalex-snapshot
Chromatin-state discovery and genome annotation with ChromHMM
inferredcites →https://doi.org/10.1038/nrg.2017.101openalex-snapshot
Genetic architecture: the shape of the genetic contribution to human traits and disease
inferredcites →https://doi.org/10.1038/nrg.2018.4openalex-snapshot
Integrative omics for health and disease
inferredcites →https://doi.org/10.1038/nrm3949openalex-snapshot
The selection and function of cell type-specific enhancers
inferredcites →https://doi.org/10.1038/s41598-017-05266-4openalex-snapshot
Single-cell transcriptomics of East-Asian pancreatic islets cells
inferredcites →https://doi.org/10.1038/s41598-017-12335-1openalex-snapshot
Alpha TC1 and Beta-TC-6 genomic profiling uncovers both shared and distinct transcriptional regulatory features with their primary islet counterparts
inferredcites →https://doi.org/10.1073/pnas.1317023110openalex-snapshot
Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants
inferredcites →https://doi.org/10.1073/pnas.1402665111openalex-snapshot
Global genomic and transcriptomic analysis of human pancreatic islets reveals novel genes influencing glucose metabolism
inferredcites →https://doi.org/10.1073/pnas.1621192114openalex-snapshot
Genetic regulatory signatures underlying islet gene expression and type 2 diabetes
inferredcites →https://doi.org/10.1074/jbc.m610553200openalex-snapshot
Glucose-stimulated Cdc42 Signaling Is Essential for the Second Phase of Insulin Secretion
inferredcites →https://doi.org/10.1080/19382014.2017.1296995openalex-snapshot
EndoC-βH1 cells display increased sensitivity to sodium palmitate when cultured in DMEM/F12 medium
inferredcites →https://doi.org/10.1084/jem.20170416openalex-snapshot
The chromatin accessibility signature of human immune aging stems from CD8+ T cells
inferredcites →https://doi.org/10.1086/519795openalex-snapshot
PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses
inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/bioinformatics/btq033openalex-snapshot
BEDTools: a flexible suite of utilities for comparing genomic features
inferredcites →https://doi.org/10.1093/bioinformatics/bts635openalex-snapshot
STAR: ultrafast universal RNA-seq aligner
inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot
Trimmomatic: a flexible trimmer for Illumina sequence data
inferredcites →https://doi.org/10.1093/bioinformatics/btu379openalex-snapshot
Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures
inferredcites →https://doi.org/10.1093/bioinformatics/btv201openalex-snapshot
GREGOR: evaluating global enrichment of trait-associated variants in epigenomic features using a systematic, data-driven approach
inferredcites →https://doi.org/10.1093/hmg/ddp209openalex-snapshot
AIP-1 ameliorates β-amyloid peptide toxicity in a Caenorhabditis elegans Alzheimer's disease model
inferredcites →https://doi.org/10.1093/hmg/ddv264openalex-snapshot
Recent advances in understanding the genetic architecture of type 2 diabetes
inferredcites →https://doi.org/10.1093/nar/gku365openalex-snapshot
deepTools: a flexible platform for exploring deep-sequencing data
inferredcites →https://doi.org/10.1093/nar/gkw1133openalex-snapshot
The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog)
inferredcites →https://doi.org/10.1093/nar/gkw809openalex-snapshot
ChIA-PET2: a versatile and flexible pipeline for ChIA-PET data analysis
inferredcites →https://doi.org/10.1096/fj.201700197rropenalex-snapshot
Regulator of G‐protein signaling Gβ5‐R7 is a crucial activator of muscarinic M3 receptor‐stimulated insulin secretion
inferredcites →https://doi.org/10.1101/192922openalex-snapshot
Chromatin accessibility profiling uncovers genetic- and T2D disease state-associated changes in cis -regulatory element use in human islets
inferredcites →https://doi.org/10.1101/245506openalex-snapshot
Fine-mapping of an expanded set of type 2 diabetes loci to single-variant resolution using high-density imputation and islet-specific epigenome maps
inferredcites →https://doi.org/10.1101/gad.1752608openalex-snapshot
Dynamic regulation of Pdx1 enhancers by Foxa1 and Foxa2 is essential for pancreas development
inferredcites →https://doi.org/10.1101/gr.150706.112openalex-snapshot
Cell-type, allelic, and genetic signatures in the human pancreatic beta cell transcriptome
inferredcites →https://doi.org/10.1101/gr.212720.116openalex-snapshot
Single-cell transcriptomes identify human islet cell signatures and reveal cell-type–specific expression changes in type 2 diabetes
inferredcites →https://doi.org/10.1111/joim.12606openalex-snapshot
The role of complement inhibitors beyond controlling inflammation
inferredcites →https://doi.org/10.1152/ajpregu.00544.2014openalex-snapshot
Distinct differences in the responses of the human pancreatic β-cell line EndoC-βH1 and human islets to proinflammatory cytokines
inferredcites →https://doi.org/10.1155/2017/2309630openalex-snapshot
Dynamics of Insulin Secretion from EndoC-βH1β-Cell Pseudoislets in Response to Glucose and Other Nutrient and Nonnutrient Secretagogues
inferredcites →https://doi.org/10.1172/jci58447openalex-snapshot
A genetically engineered human pancreatic β cell line exhibiting glucose-inducible insulin secretion
inferredcites →https://doi.org/10.1172/jci66514openalex-snapshot
Epigenomic plasticity enables human pancreatic α to β cell reprogramming
inferredcites →https://doi.org/10.1172/jci91304openalex-snapshot
β Cells led astray by transcription factors and the company they keep
inferredcites →https://doi.org/10.1182/blood-2015-04-643270openalex-snapshot
Essential control of early B-cell development by Mef2 transcription factors
inferredcites →https://doi.org/10.1186/1471-2164-15-s1-s11openalex-snapshot
Genome sequencing of high-penicillin producing industrial strain of Penicillium chrysogenum
inferredcites →https://doi.org/10.1186/1471-2164-15-s12-s11openalex-snapshot
Chromatin Interaction Analysis with Paired-End Tag (ChIA-PET) sequencing technology and application
inferredcites →https://doi.org/10.1186/2045-9769-3-7openalex-snapshot
Role of Oct4 in the early embryo development
inferredcites →https://doi.org/10.1186/gb-2008-9-9-r137openalex-snapshot
Model-based Analysis of ChIP-Seq (MACS)
inferredcites →https://doi.org/10.1186/s12859-015-0670-5openalex-snapshot
QoRTs: a comprehensive toolset for quality control and data processing of RNA-Seq experiments
inferredcites →https://doi.org/10.1210/me.2003-0371openalex-snapshot
Conserved Transcriptional Regulatory Domains of the pdx-1 Gene
inferredcites →https://doi.org/10.1210/me.2015-1227openalex-snapshot
Molecular Genetic Regulation of Slc30a8/ZnT8 Reveals a Positive Association With Glucose Tolerance
inferredcites →https://doi.org/10.1242/dev.095927openalex-snapshot
Oct transcription factors in development and stem cells: insights and mechanisms
inferredcites →https://doi.org/10.1242/dev.096875openalex-snapshot
Oct4 is required for lineage priming in the developing inner cell mass of the mouse blastocyst
inferredcites →https://doi.org/10.1242/dev.104810openalex-snapshot
Insm1 promotes endocrine cell differentiation by modulating the expression of a network of genes that includes Neurog3 and Ripply3
inferredcites →https://doi.org/10.12688/f1000research.8759.2openalex-snapshot
Infrastructure for genomic interactions: Bioconductor classes for Hi-C, ChIA-PET and related experiments
inferredcites →https://doi.org/10.1371/journal.pgen.1004160openalex-snapshot
Genome-Wide DNA Methylation Analysis of Human Pancreatic Islets from Type 2 Diabetic and Non-Diabetic Donors Identifies Candidate Genes That Influence Insulin Secretion
inferredcites →https://doi.org/10.1371/journal.pgen.1005694openalex-snapshot
Transcript Expression Data from Human Islets Links Regulatory Signals from Genome-Wide Association Studies for Type 2 Diabetes and Glycemic Traits to Their Downstream Effectors
inferredcites →https://doi.org/10.1371/journal.pone.0055272openalex-snapshot
The miRNA Profile of Human Pancreatic Islets and Beta-Cells and Relationship to Type 2 Diabetes Pathogenesis
inferredcites →https://doi.org/10.1371/journal.pone.0120879openalex-snapshot
Characterization of Stimulus-Secretion Coupling in the Human Pancreatic EndoC-βH1 Beta Cell Line
inferredcites →https://doi.org/10.1371/journal.pone.0175355openalex-snapshot
Expression and localization of sterile alpha motif domain containing 5 is associated with cell type and malignancy of biliary tree
inferredcites →https://doi.org/10.1515/jib-2016-307openalex-snapshot
miRquant 2.0: an Expanded Tool for Accurate Annotation and Quantification of MicroRNAs and their isomiRs from Small RNA-Sequencing Data
inferredcites →https://doi.org/10.15252/embr.201540946openalex-snapshot
Single‐cell transcriptomes reveal characteristic features of human pancreatic islet cell types
inferredcites →https://doi.org/10.2337/db14-1443openalex-snapshot
Tshz1 Regulates Pancreatic β-Cell Maturation
inferredcites →https://doi.org/10.2337/db15-0039openalex-snapshot
Novel Observations From Next-Generation RNA Sequencing of Highly Purified Human Adult and Fetal Islet Cell Subsets
inferredcites →https://doi.org/10.2337/db16-0405openalex-snapshot
Single-Cell Transcriptomics of the Human Endocrine Pancreas
inferredcites →https://doi.org/10.6084/m9.figshare.963153.v1openalex-snapshot
Aligning sequence reads, clone sequences and assembly con*gs with BWA-MEM
inferredcites →https://doi.org/10.7554/elife.26174openalex-snapshot
Exophilin-8 assembles secretory granules for exocytosis in the actin cortex via interaction with RIM-BP2 and myosin-VIIa

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1038/s41598-018-34420-9openalex-snapshot
A neural network based model effectively predicts enhancers from clinical ATAC-seq samples
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