Literature DB >> 33137644

PlacentaCellEnrich: A tool to characterize gene sets using placenta cell-specific gene enrichment analysis.

Ashish Jain1, Geetu Tuteja2.   

Abstract

Single-cell RNA-Sequencing (scRNA-Seq) has improved our understanding of individual cell types in the human placenta. However, placental scRNA-Seq data is not readily accessible when trying to understand how expression patterns in model systems correspond to those from first trimester human placenta. Therefore, we developed PlacentaCellEnrich, a tool that takes a gene set as input, and then reports if the input set is enriched for genes with placenta cell-specific expression patterns, based on human placenta scRNA-Seq data. The PlacentaCellEnrich tool is freely available at https://placentacellenrich.gdcb.iastate.edu/ for non-profit academic use under the MIT license.
Copyright © 2020 Elsevier Ltd. All rights reserved.

Entities:  

Keywords:  Cell subtype identification; Decidua; Gene enrichment; Trophoblast; scRNA-seq

Mesh:

Substances:

Year:  2020        PMID: 33137644      PMCID: PMC7920947          DOI: 10.1016/j.placenta.2020.10.029

Source DB:  PubMed          Journal:  Placenta        ISSN: 0143-4004            Impact factor:   3.481


  28 in total

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Journal:  Nature       Date:  2018-11-14       Impact factor: 69.504

6.  Deciphering transcriptional regulation in human embryonic stem cells specified towards a trophoblast fate.

Authors:  Ashish Jain; Toshihiko Ezashi; R Michael Roberts; Geetu Tuteja
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7.  A single-cell survey of the human first-trimester placenta and decidua.

Authors:  Hemant Suryawanshi; Pavel Morozov; Alexander Straus; Nicole Sahasrabudhe; Klaas E A Max; Aitor Garzia; Manjunath Kustagi; Thomas Tuschl; Zev Williams
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8.  Early onset preeclampsia in a model for human placental trophoblast.

Authors:  Megan A Sheridan; Ying Yang; Ashish Jain; Alex S Lyons; Penghua Yang; Sambasiva R Brahmasani; Aihua Dai; Yuchen Tian; Mark R Ellersieck; Geetu Tuteja; Danny J Schust; Laura C Schulz; Toshihiko Ezashi; R Michael Roberts
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1.  Conservation at the uterine-placental interface.

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2.  Gene expression phylogenies and ancestral transcriptome reconstruction resolves major transitions in the origins of pregnancy.

Authors:  Katelyn Mika; Camilla M Whittington; Bronwyn M McAllan; Vincent J Lynch
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3.  The product of BMP-directed differentiation protocols for human primed pluripotent stem cells is placental trophoblast and not amnion.

Authors:  Arun S Seetharam; Ha T H Vu; Sehee Choi; Teka Khan; Megan A Sheridan; Toshihiko Ezashi; R Michael Roberts; Geetu Tuteja
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4.  Derivation of functional trophoblast stem cells from primed human pluripotent stem cells.

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5.  Induction of human trophoblast stem-like cells from primed pluripotent stem cells.

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Review 6.  Leveraging Optimized Transcriptomic and Personalized Stem Cell Technologies to Better Understand Syncytialization Defects in Preeclampsia.

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8.  Reliability of a novel approach for reference-based cell type estimation in human placental DNA methylation studies.

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9.  Single Nucleus RNA Sequence (snRNAseq) Analysis of the Spectrum of Trophoblast Lineages Generated From Human Pluripotent Stem Cells in vitro.

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  9 in total

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