Abstract

Single-cell and single-nucleus RNA sequencing have been widely adopted in studies of heterogeneous tissues to estimate their cellular composition and obtain transcriptional profiles of individual cells. However, the current fragmentary understanding of artefacts introduced by sample preparation protocols impedes the selection of optimal workflows and compromises data interpretation. To bridge this gap, we compared performance of several workflows applied to adult mouse kidneys. Our study encompasses two tissue dissociation protocols, two cell preservation methods, bulk tissue RNA sequencing, single-cell and three single-nucleus RNA sequencing workflows for the 10x Genomics Chromium platform. These experiments enable a systematic comparison of recovered cell types and their transcriptional profiles across the workflows and highlight protocol-specific biases important for the experimental design and data interpretation.
Original languageEnglish
Article number832444
Pages (from-to)1-47
Number of pages47
JournalbioRxiv
Publication statusSubmitted - 6 Nov 2019

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Small Cytoplasmic RNA
Workflow
RNA Sequence Analysis
Chromium
Genomics
Cell Nucleus
Artifacts
Research Design
Kidney

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title = "Systematic bias assessment in solid tissue 10x scRNA-seq workflows",
abstract = "Single-cell and single-nucleus RNA sequencing have been widely adopted in studies of heterogeneous tissues to estimate their cellular composition and obtain transcriptional profiles of individual cells. However, the current fragmentary understanding of artefacts introduced by sample preparation protocols impedes the selection of optimal workflows and compromises data interpretation. To bridge this gap, we compared performance of several workflows applied to adult mouse kidneys. Our study encompasses two tissue dissociation protocols, two cell preservation methods, bulk tissue RNA sequencing, single-cell and three single-nucleus RNA sequencing workflows for the 10x Genomics Chromium platform. These experiments enable a systematic comparison of recovered cell types and their transcriptional profiles across the workflows and highlight protocol-specific biases important for the experimental design and data interpretation.",
author = "Elena Denisenko and Belinda Guo and Matthew Jones and Rui Hou and {De Kock}, Leanne and Timo Lassmann and Daniel Poppe and Olivier Clement and Simmons, {Rebecca K.} and Ryan Lister and Alistair Forrest",
year = "2019",
month = "11",
day = "6",
language = "English",
pages = "1--47",
journal = "bioRxiv",
publisher = "Cold Spring Harbor Laboratory",

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T1 - Systematic bias assessment in solid tissue 10x scRNA-seq workflows

AU - Denisenko, Elena

AU - Guo, Belinda

AU - Jones, Matthew

AU - Hou, Rui

AU - De Kock, Leanne

AU - Lassmann, Timo

AU - Poppe, Daniel

AU - Clement, Olivier

AU - Simmons, Rebecca K.

AU - Lister, Ryan

AU - Forrest, Alistair

PY - 2019/11/6

Y1 - 2019/11/6

N2 - Single-cell and single-nucleus RNA sequencing have been widely adopted in studies of heterogeneous tissues to estimate their cellular composition and obtain transcriptional profiles of individual cells. However, the current fragmentary understanding of artefacts introduced by sample preparation protocols impedes the selection of optimal workflows and compromises data interpretation. To bridge this gap, we compared performance of several workflows applied to adult mouse kidneys. Our study encompasses two tissue dissociation protocols, two cell preservation methods, bulk tissue RNA sequencing, single-cell and three single-nucleus RNA sequencing workflows for the 10x Genomics Chromium platform. These experiments enable a systematic comparison of recovered cell types and their transcriptional profiles across the workflows and highlight protocol-specific biases important for the experimental design and data interpretation.

AB - Single-cell and single-nucleus RNA sequencing have been widely adopted in studies of heterogeneous tissues to estimate their cellular composition and obtain transcriptional profiles of individual cells. However, the current fragmentary understanding of artefacts introduced by sample preparation protocols impedes the selection of optimal workflows and compromises data interpretation. To bridge this gap, we compared performance of several workflows applied to adult mouse kidneys. Our study encompasses two tissue dissociation protocols, two cell preservation methods, bulk tissue RNA sequencing, single-cell and three single-nucleus RNA sequencing workflows for the 10x Genomics Chromium platform. These experiments enable a systematic comparison of recovered cell types and their transcriptional profiles across the workflows and highlight protocol-specific biases important for the experimental design and data interpretation.

M3 - Article

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EP - 47

JO - bioRxiv

JF - bioRxiv

M1 - 832444

ER -