(Q36233059)

27 May 2018

title

Analysis of Transcriptional Variability in a Large Human iPSC Library Reveals Genetic and Non-genetic Determinants of Heterogeneity (English)

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27 May 2018

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21

Thomas Quertermous

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Gerald Reaven

10

object named as

Gerald M Reaven

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27 May 2018

18

Eric E Schadt

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27 May 2018

author name string

Ivan Carcamo-Orive

1

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27 May 2018

Gabriel E Hoffman

2

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27 May 2018

Paige Cundiff

3

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27 May 2018

Noam D Beckmann

4

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27 May 2018

Sunita L D'Souza

5

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27 May 2018

Joshua W Knowles

6

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27 May 2018

Achchhe Patel

7

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27 May 2018

Dimitri Papatsenko

8

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27 May 2018

Fahim Abbasi

9

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Sean Whalen

11

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27 May 2018

Philip Lee

12

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27 May 2018

Mohammad Shahbazi

13

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27 May 2018

Marc Y R Henrion

14

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27 May 2018

Kuixi Zhu

15

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27 May 2018

Sven Wang

16

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27 May 2018

Panos Roussos

17

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27 May 2018

Gaurav Pandey

19

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27 May 2018

Rui Chang

20

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27 May 2018

Ihor Lemischka

22

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27 May 2018

language of work or name

English

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publication date

22 December 2016

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27 May 2018

published in

Cell Stem Cell

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27 May 2018

volume

20

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27 May 2018

issue

4

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27 May 2018

page(s)

518-532.e9

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27 May 2018

describes a project that uses

1 reference

10 June 2022

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&rettype=xml&id=5384872

limma

1 reference

22 June 2022

https://europepmc.org/article/PMC/5384872

based on heuristic

inferred from PubMed Central ID database lookup

cites work

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1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5384872

RNA splicing is a primary link between genetic variation and disease

29 June 2018

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Genetic Variation, Not Cell Type of Origin, Underlies the Majority of Identifiable Regulatory Differences in iPSCs

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5384872

Genetic Variability Overrides the Impact of Parental Cell Type and Determines iPSC Differentiation Potential

29 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5384872

The metabolome regulates the epigenetic landscape during naive-to-primed human embryonic stem cell transition

29 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5384872

A comparison of genetically matched cell lines reveals the equivalence of human iPSCs and ESCs

29 June 2018

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29 June 2018

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PRC2 Is Required to Maintain Expression of the Maternal Gtl2-Rian-Mirg Locus by Preventing De Novo DNA Methylation in Mouse Embryonic Stem Cells

29 June 2018

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Ground State Conditions Induce Rapid Reorganization of Core Pluripotency Factor Binding before Global Epigenetic Reprogramming

29 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5384872

Human genomics. Effect of predicted protein-truncating genetic variants on the human transcriptome

29 June 2018

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Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans

29 June 2018

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Reprogramming LCLs to iPSCs Results in Recovery of Donor-Specific Gene Expression Signature

29 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5384872

Integrative analysis of 111 reference human epigenomes

29 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5384872

limma powers differential expression analyses for RNA-sequencing and microarray studies

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5384872

Deconstructing transcriptional heterogeneity in pluripotent stem cells

29 June 2018

1 reference

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29 June 2018

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DLK1-DIO3 imprinted cluster in induced pluripotency: landscape in the mist

29 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5384872

Systematic identification of culture conditions for induction and maintenance of naive human pluripotency

29 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5384872

Genetic background drives transcriptional variation in human induced pluripotent stem cells

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5384872

Interactions between JARID2 and noncoding RNAs regulate PRC2 recruitment to chromatin.

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5384872

The NHGRI GWAS Catalog, a curated resource of SNP-trait associations

29 June 2018

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featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

29 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5384872

Transcriptome and genome sequencing uncovers functional variation in humans

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5384872

Genetic and epigenetic variations in iPSCs: potential causes and implications for application

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5384872

Polycomb complexes in stem cells and embryonic development.

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5384872

Origins and implications of pluripotent stem cell variability and heterogeneity

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5384872

Integrated systems approach identifies genetic nodes and networks in late-onset Alzheimer's disease

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5384872

Cell reprogramming requires silencing of a core subset of polycomb targets

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5384872

Dynamic chromatin remodeling mediated by polycomb proteins orchestrates pancreatic differentiation of human embryonic stem cells

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5384872

The ConsensusPathDB interaction database: 2013 update

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5384872

STAR: ultrafast universal RNA-seq aligner

29 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5384872

BEDOPS: high-performance genomic feature operations

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5384872

Recurrent variations in DNA methylation in human pluripotent stem cells and their differentiated derivatives.

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5384872

Stitching together multiple data dimensions reveals interacting metabolomic and transcriptomic networks that modulate cell regulation

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5384872

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29 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5384872

A linear complexity phasing method for thousands of genomes

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5384872

Genetic variants in novel pathways influence blood pressure and cardiovascular disease risk

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5384872

Large-scale analysis reveals acquisition of lineage-specific chromosomal aberrations in human adult stem cells

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5384872

Epigenetic memory and preferential lineage-specific differentiation in induced pluripotent stem cells derived from human pancreatic islet beta cells

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5384872

A framework for variation discovery and genotyping using next-generation DNA sequencing data

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5384872

A bioinformatic assay for pluripotency in human cells

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5384872

HTSanalyzeR: an R/Bioconductor package for integrated network analysis of high-throughput screens.

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5384872

Temporal changes in Hox gene expression accompany endothelial cell differentiation of embryonic stem cells

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5384872

Polycomb group proteins set the stage for early lineage commitment

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5384872

Epigenetic memory in induced pluripotent stem cells

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5384872

LocusZoom: regional visualization of genome-wide association scan results

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5384872

Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5384872

A Bayesian framework to account for complex non-genetic factors in gene expression levels greatly increases power in eQTL studies

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5384872

Aberrant silencing of imprinted genes on chromosome 12qF1 in mouse induced pluripotent stem cells

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5384872

Activation of the imprinted Dlk1-Dio3 region correlates with pluripotency levels of mouse stem cells

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5384872

A scaling normalization method for differential expression analysis of RNA-seq data

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5384872

Gene ontology analysis for RNA-seq: accounting for selection bias

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5384872

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5384872

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5384872

A flexible and accurate genotype imputation method for the next generation of genome-wide association studies

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5384872

GAGE: generally applicable gene set enrichment for pathway analysis

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5384872

WGCNA: an R package for weighted correlation network analysis

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5384872

Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5384872

Juxtaposed Polycomb complexes co-regulate vertebral identity

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5384872

Polycomb complexes repress developmental regulators in murine embryonic stem cells

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5384872

Genome-wide mapping of Polycomb target genes unravels their roles in cell fate transitions

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5384872

A role for Hox A5 in regulating angiogenesis and vascular patterning

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5384872

Derivation of novel human ground state naive pluripotent stem cells

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5384872

Identification and Classification of Chromosomal Aberrations in Human Induced Pluripotent Stem Cells

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5384872

10.1016/J.STEM.2016.11.005

21 October 2018

Identifiers

DOI

1 reference

27 May 2018

PMC publication ID

5384872

1 reference

27 May 2018

PubMed publication ID

28017796

1 reference

27 May 2018