Characterization of transcript enrichment and detection bias in single-nucleus RNA-seq for mapping of distinct human adipocyte lineages

Benchmarking atlas-level data integration in single-cell genomics

(2021) Malte D. Luecken et al.   NATURE METHODS

Single cell approaches to address adipose tissue stromal cell heterogeneity

(2020) Elizabeth A. Rondini et al.   BIOCHEMICAL JOURNAL

SLIM: Simultaneous Logic-in-Memory Computing Exploiting Bilayer Analog OxRAM Devices

(2020) Sandeep Kaur Kingra et al.   Scientific Reports

TGF-β/SMAD signaling regulation of mesenchymal stem cells in adipocyte commitment

(2020) Sheng-Nan Li et al.   Stem Cell Research & Therapy

The role and possible mechanism of long noncoding RNA PVT1 in modulating 3T3‐L1 preadipocyte proliferation and differentiation

(2020) Lin Zhang et al.   IUBMB LIFE

Benchmarking single-cell RNA-sequencing protocols for cell atlas projects

(2020) Elisabetta Mereu et al.   NATURE BIOTECHNOLOGY

A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors

(2020) Michal Slyper et al.   NATURE MEDICINE

A Landscape of Murine Long Non-Coding RNAs Reveals the Leading Transcriptome Alterations in Adipose Tissue during Aging

(2020) Qiuzhong Zhou et al.   Cell Reports

An Emerging Class of Long Non-coding RNA With Oncogenic Role Arises From the snoRNA Host Genes

(2020) Alina-Andreea Zimta et al.   Frontiers in Oncology

The Impact of Single-Cell Genomics on Adipose Tissue Research

(2020) Alana Deutsch et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Enhancing droplet-based single-nucleus RNA-seq resolution using the semi-supervised machine learning classifier DIEM

(2020) Marcus Alvarez et al.   Scientific Reports

Single-Cell RNA Profiling Reveals Adipocyte to Macrophage Signaling Sufficient to Enhance Thermogenesis

(2020) Felipe Henriques et al.   Cell Reports

Toward a Consensus View of Mammalian Adipocyte Stem and Progenitor Cell Heterogeneity

(2020) Radiana Ferrero et al.   TRENDS IN CELL BIOLOGY

Single-Nucleus RNA-Seq Is Not Suitable for Detection of Microglial Activation Genes in Humans

(2020) Nicola Thrupp et al.   Cell Reports

Plasticity of Epididymal Adipose Tissue in Response to Diet-Induced Obesity at Single-Nucleus Resolution

(2020) Anitta Kinga Sárvári et al.   Cell Metabolism

Adipogenesis and metabolic health

(2019) Alexandra L. Ghaben et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Function and Mechanism of Long Noncoding RNAs in Adipocyte Biology

(2019) Lei Sun et al.   DIABETES

Identification of a mesenchymal progenitor cell hierarchy in adipose tissue

(2019) David Merrick et al.   SCIENCE

lncRNA Spehd Regulates Hematopoietic Stem and Progenitor Cells and Is Required for Multilineage Differentiation

(2019) M. Joaquina Delás et al.   Cell Reports

Single-Cell RNA-Sequencing and Metabolomics Analyses Reveal the Contribution of Perivascular Adipose Tissue Stem Cells to Vascular Remodeling

(2019) Wenduo Gu et al.   ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Lipid-Associated Macrophages Control Metabolic Homeostasis in a Trem2-Dependent Manner

(2019) Diego Adhemar Jaitin et al.   CELL

Nuclei multiplexing with barcoded antibodies for single-nucleus genomics

(2019) Jellert T. Gaublomme et al.   Nature Communications

Cell-type-specific analysis of alternative polyadenylation using single-cell transcriptomics data

(2019) Eldad David Shulman et al.   NUCLEIC ACIDS RESEARCH

Low- and high-thermogenic brown adipocyte subpopulations coexist in murine adipose tissue

(2019) Anying Song et al.   JOURNAL OF CLINICAL INVESTIGATION

Functional interpretation of single cell similarity maps

(2019) David DeTomaso et al.   Nature Communications

Single cell analysis reveals immune cell–adipocyte crosstalk regulating the transcription of thermogenic adipocytes

(2019) Prashant Rajbhandari et al.   eLife

Dosage Compensation of the X Chromosome: A Complex Epigenetic Assignment Involving Chromatin Regulators and Long Noncoding RNAs

(2018) Maria Samata et al.   Annual Review of Biochemistry

Actomyosin-Mediated Tension Orchestrates Uncoupled Respiration in Adipose Tissues

(2018) Kevin M. Tharp et al.   Cell Metabolism

Deconstructing Adipogenesis Induced by β3-Adrenergic Receptor Activation with Single-Cell Expression Profiling

(2018) Rayanne B. Burl et al.   Cell Metabolism

S100A4 protects mice from high-fat diet-induced obesity and inflammation

(2018) Shasha Hou et al.   LABORATORY INVESTIGATION

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

De novo reconstruction of human adipose transcriptome reveals conserved lncRNAs as regulators of brown adipogenesis

(2018) Chunming Ding et al.   Nature Communications

No evidence that carotenoid pigments boost either immune or antioxidant defenses in a songbird

(2018) Rebecca E. Koch et al.   Nature Communications

Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database

(2018) Luke Zappia et al.   PLoS Computational Biology

zUMIs - A fast and flexible pipeline to process RNA sequencing data with UMIs

(2018) Swati Parekh et al.   GigaScience

Power in Numbers: Single-Cell RNA-Seq Strategies to Dissect Complex Tissues

(2018) Kenneth D. Birnbaum   Annual Review of Genetics

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

A stromal cell population that inhibits adipogenesis in mammalian fat depots

(2018) Petra C. Schwalie et al.   NATURE

Flow Cytometry of Mouse and Human Adipocytes for the Analysis of Browning and Cellular Heterogeneity

(2018) Carolina E. Hagberg et al.   Cell Reports

FSP1-positive fibroblasts are adipogenic niche and regulate adipose homeostasis

(2018) Rui Zhang et al.   PLOS BIOLOGY

Identification of functionally distinct fibro-inflammatory and adipogenic stromal subpopulations in visceral adipose tissue of adult mice

(2018) Chelsea Hepler et al.   eLife

Developmental and functional heterogeneity of white adipocytes within a single fat depot

(2018) Kevin Y Lee et al.   EMBO JOURNAL

Advantages of Single-Nucleus over Single-Cell RNA Sequencing of Adult Kidney: Rare Cell Types and Novel Cell States Revealed in Fibrosis

(2018) Haojia Wu et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris

(2018) et al.   NATURE

Deep generative modeling for single-cell transcriptomics

(2018) Romain Lopez et al.   NATURE METHODS

Single-nucleus and single-cell transcriptomes compared in matched cortical cell types

(2018) Trygve E. Bakken et al.   PLoS One

Long non-coding RNA MEG3 inhibits adipogenesis and promotes osteogenesis of human adipose-derived mesenchymal stem cells via miR-140-5p

(2017) Zheng Li et al.   MOLECULAR AND CELLULAR BIOCHEMISTRY

Massively parallel single-nucleus RNA-seq with DroNc-seq

(2017) Naomi Habib et al.   NATURE METHODS

Noncoding RNAs in the Regulation of Pluripotency and Reprogramming

(2017) Vladimir V. Sherstyuk et al.   Stem Cell Reviews and Reports

CD36 Is a Marker of Human Adipocyte Progenitors with Pronounced Adipogenic and Triglyceride Accumulation Potential

(2017) Hui Gao et al.   STEM CELLS

Single cell transcriptomics suggest that human adipocyte progenitor cells constitute a homogeneous cell population

(2017) Juan R. Acosta et al.   Stem Cell Research & Therapy

Cell Surface Markers on Adipose-Derived Stem Cells: A Systematic Review

(2017) Alexander Mildmay-White et al.   Current Stem Cell Research & Therapy

Comprehensive analysis of nucleocytoplasmic dynamics of mRNA in Drosophila cells

(2017) Tao Chen et al.   PLoS Genetics

Noncoding RNAs in the Regulation of Pluripotency and Reprogramming

(2017) Vladimir V. Sherstyuk et al.   Stem Cell Reviews and Reports

The dual role of BMP4 in adipogenesis and metabolism

(2017) Salvatore Modica et al.   Adipocyte

Optical visualisation of thermogenesis in stimulated single-cell brown adipocytes

(2017) Rókus Kriszt et al.   Scientific Reports

A comparative strategy for single-nucleus and single-cell transcriptomes confirms accuracy in predicted cell-type expression from nuclear RNA

(2017) Blue B. Lake et al.   Scientific Reports

Knockdown of lncRNA MIR31HG inhibits adipocyte differentiation of human adipose-derived stem cells via histone modification of FABP4

(2017) Yiping Huang et al.   Scientific Reports

FastProject: a tool for low-dimensional analysis of single-cell RNA-Seq data

(2016) David DeTomaso et al.   BMC BIOINFORMATICS

Long noncoding RNAs in regulating adipogenesis: new RNAs shed lights on obesity

(2016) Shengjuan Wei et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Single-cell transcriptomics and functional target validation of brown adipocytes show their complex roles in metabolic homeostasis

(2016) Jennifer M. Spaethling et al.   FASEB JOURNAL

Ectopic and Visceral Fat Deposition in Lean and Obese Patients With Type 2 Diabetes

(2016) Eylem Levelt et al.   JOURNAL OF THE AMERICAN COLLEGE OF CARDIOLOGY

Human 'brite/beige' adipocytes develop from capillary networks and their implantation improves metabolic homeostasis in mice

(2016) So Yun Min et al.   NATURE MEDICINE

Single-nucleus RNA-seq of differentiating human myoblasts reveals the extent of fate heterogeneity

(2016) Weihua Zeng et al.   NUCLEIC ACIDS RESEARCH

Emerging Complexities in Adipocyte Origins and Identity

(2016) Joan Sanchez-Gurmaches et al.   TRENDS IN CELL BIOLOGY

GeneBase 1.1: a tool to summarize data from NCBI gene datasets and its application to an update of human gene statistics

(2016) Allison Piovesan et al.   Database-The Journal of Biological Databases and Curation

A stringent validation of mouse adipose tissue identity markers

(2015) Jasper M. A. de Jong et al.   AMERICAN JOURNAL OF PHYSIOLOGY-ENDOCRINOLOGY AND METABOLISM

Brown, Beige, and White: The New Color Code of Fat and Its Pharmacological Implications

(2015) Alexander Pfeifer et al.   Annual Review of Pharmacology and Toxicology

Defining cell types and states with single-cell genomics

(2015) Cole Trapnell   GENOME RESEARCH

Mesoderm-specific transcript (MEST) is a negative regulator of human adipocyte differentiation

(2015) M Karbiener et al.   INTERNATIONAL JOURNAL OF OBESITY

Analysis of intronic and exonic reads in RNA-seq data characterizes transcriptional and post-transcriptional regulation

(2015) Dimos Gaidatzis et al.   NATURE BIOTECHNOLOGY

Clonal analyses and gene profiling identify genetic biomarkers of the thermogenic potential of human brown and white preadipocytes

(2015) Ruidan Xue et al.   NATURE MEDICINE

Genetic and functional characterization of clonally derived adult human brown adipocytes

(2015) Kosaku Shinoda et al.   NATURE MEDICINE

YAP and TAZ: a nexus for Hippo signaling and beyond

(2015) Carsten Gram Hansen et al.   TRENDS IN CELL BIOLOGY

Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution

(2015) Moran N Cabili et al.   GENOME BIOLOGY

Fra-2/AP-1 controls adipocyte differentiation and survival by regulating PPARγ and hypoxia

(2014) J Luther et al.   CELL DEATH AND DIFFERENTIATION

Id transcriptional regulators in adipogenesis and adipose tissue metabolism

(2014) Mallikarjun Patil   Frontiers in Bioscience-Landmark

Follistatin promotes adipocyte differentiation, browning, and energy metabolism

(2014) Melissa Braga et al.   JOURNAL OF LIPID RESEARCH

Comparative gene array analysis of progenitor cells from human paired deep neck and subcutaneous adipose tissue

(2014) D. Tews et al.   MOLECULAR AND CELLULAR ENDOCRINOLOGY

Extensive Oscillatory Gene Expression during C. elegans Larval Development

(2014) Gert-Jan Hendriks et al.   MOLECULAR CELL

Selective nuclear export of specific classes of mRNA from mammalian nuclei is promoted by GANP

(2014) Vihandha O. Wickramasinghe et al.   NUCLEIC ACIDS RESEARCH

SnapShot-Seq: A Method for Extracting Genome-Wide, In Vivo mRNA Dynamics from a Single Total RNA Sample

(2014) Jesse M. Gray et al.   PLoS One

FindFoci: A Focus Detection Algorithm with Automated Parameter Training That Closely Matches Human Assignments, Reduces Human Inconsistencies and Increases Speed of Analysis

(2014) Alex D. Herbert et al.   PLoS One

Long noncoding RNAs: an emerging link between gene regulation and nuclear organization

(2014) Sofia Quinodoz et al.   TRENDS IN CELL BIOLOGY

Identification of the transcription factor ZEB1 as a central component of the adipogenic gene regulatory network

(2014) Carine Gubelmann et al.   eLife

Beyond the Sympathetic Tone: The New Brown Fat Activators

(2013) Francesc Villarroya et al.   Cell Metabolism

Characterization of the adipocyte cellular lineage in vivo

(2013) Ryan Berry et al.   NATURE CELL BIOLOGY

Evidence for two types of brown adipose tissue in humans

(2013) Martin E Lidell et al.   NATURE MEDICINE

RNA-sequencing from single nuclei

(2013) R. V. Grindberg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Long noncoding RNAs regulate adipogenesis

(2013) Lei Sun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Regulation of the Hippo-YAP Pathway by G-Protein-Coupled Receptor Signaling

(2012) Fa-Xing Yu et al.   CELL

Origins of metabolic complications in obesity

(2011) Stefania Carobbio et al.   CURRENT OPINION IN CLINICAL NUTRITION AND METABOLIC CARE

Ablation of the transcriptional regulator Id1 enhances energy expenditure, increases insulin sensitivity, and protects against age and diet induced insulin resistance, and hepatosteatosis

(2011) Ande Satyanarayana et al.   FASEB JOURNAL

Elevated Fra-1 expression causes severe lipodystrophy

(2011) J. Luther et al.   JOURNAL OF CELL SCIENCE

Adipose tissue stem cells meet preadipocyte commitment: going back to the future

(2011) William P. Cawthorn et al.   JOURNAL OF LIPID RESEARCH

Role of YAP/TAZ in mechanotransduction

(2011) Sirio Dupont et al.   NATURE

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

(2011) Adam Ameur et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

On the Role of FOX Transcription Factors in Adipocyte Differentiation and Insulin-stimulated Glucose Uptake

(2009) Isabelle Gerin et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Role of Insulin-Like Growth Factor-Binding Protein 5 (IGFBP5) in Organismal and Pancreatic β-Cell Growth

(2009) Catherine E. Gleason et al.   MOLECULAR ENDOCRINOLOGY

Hypertrophy and/or Hyperplasia: Dynamics of Adipose Tissue Growth

(2009) Junghyo Jo et al.   PLoS Computational Biology

Imaging individual mRNA molecules using multiple singly labeled probes

(2008) Arjun Raj et al.   NATURE METHODS