High-throughput scNMT protocol for multiomics profiling of single cells from mouse brain and pancreatic organoids

High-throughput scNMT protocol for multiomics profiling of single cells from mouse brain and pancreatic organoids

Summary: Single-cell nucleosome, methylome, and transcriptome (scNMT) sequencing is a recently developed method that allows multiomics profiling of single cells. In this scNMT protocol, we describe profiling of cells from mouse brain and pancreatic organoids, using liquid handling platforms to incre...

Full description

Bibliographic Details
Main Authors:	Santiago Cerrizuela, Oguzhan Kaya, Lukas P.M. Kremer, Andrea Sarvari, Tobias Ellinger, Jannes Straub, Jan Brunken, Andrés Sanz-Morejón, Aylin Korkmaz, Ana Martín-Villalba
Format:	Article
Language:	English
Published:	Elsevier 2022-09-01
Series:	STAR Protocols
Subjects:	Bioinformatics Sequence analysis Cell Biology Single Cell Genomics Sequencing
Online Access:	http://www.sciencedirect.com/science/article/pii/S266616672200435X

Similar Items

scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells
by: Stephen J. Clark, et al.
Published: (2018-02-01)

Visual Genomics Analysis Studio as a Tool to Analyze Multiomic Data
by: Rebecca J. Hertzman, et al.
Published: (2021-06-01)

Novel Human Meningioma Organoids Recapitulate the Aggressiveness of the Initiating Cell Subpopulations Identified by ScRNA‐Seq
by: Meng Huang, et al.
Published: (2023-05-01)

Protocol for the isolation and single-nuclei multiomic analyses of the human fetal epicardium
by: Stanislao Igor Travisano, et al.
Published: (2024-06-01)

Optimized workflow for human PBMC multiomic immunosurveillance studies
by: Palak C. Genge, et al.
Published: (2021-12-01)

Single-cell transcriptomics of lung organoids
by: Ye Na Song, et al.
Published: (2021-10-01)

scGR-seq: Integrated analysis of glycan and RNA in single cells
by: Haruki Odaka, et al.
Published: (2022-03-01)

Identification and Tracking of Alloreactive T Cell Clones in Rhesus Macaques Through the RM-scTCR-Seq Platform
by: Ulrike Gerdemann, et al.
Published: (2022-01-01)

Single-Cell Multiomic Approaches Reveal Diverse Labeling of the Nervous System by Common Cre-Drivers
by: Rachel A. Keuls, et al.
Published: (2021-04-01)

Characterization and Optimization of Multiomic Single-Cell Epigenomic Profiling
by: Leticia Sandoval, et al.
Published: (2023-06-01)

ScRNA-seq and ST-seq in liver research
by: Jia He, et al.
Published: (2023-02-01)

Coupled scRNA-seq and Bulk-seq reveal the role of HMMR in hepatocellular carcinoma
by: Zhixiong Su, et al.
Published: (2024-04-01)

Differentiation and single-cell RNA-seq analyses of human pluripotent-stem-cell-derived renal organoids
by: Eric Lian, et al.
Published: (2023-06-01)

scTyper: a comprehensive pipeline for the cell typing analysis of single-cell RNA-seq data
by: Ji-Hye Choi, et al.
Published: (2020-08-01)

mSphere of Influence: Organoids and Single-Cell Sequencing, a Powerful Combination To Uncover Epithelial and Immune Cell Interactions in the Human Gut Environment
by: Jose M. Lemme-Dumit
Published: (2020-08-01)

Analyzing genomic and epigenetic profiles in single cells by hybrid transposase (scGET-seq)
by: Davide Cittaro, et al.
Published: (2023-06-01)

The challenges and opportunities of scRNA-seq in COVID-19 research and clinical translation
by: Wendao Liu, et al.
Published: (2022-12-01)

Protocol for the isolation of CD8+ tumor-infiltrating lymphocytes from human tumors and their characterization by single-cell immune profiling and multiome
by: Carmen M. Anadon, et al.
Published: (2022-09-01)

Organoid research on human early development and beyond
by: Wen Lu, et al.
Published: (2022-10-01)

Clustering Deviation Index (CDI): a robust and accurate internal measure for evaluating scRNA-seq data clustering
by: Jiyuan Fang, et al.
Published: (2022-12-01)

scQCEA: a framework for annotation and quality control report of single-cell RNA-sequencing data
by: Isar Nassiri, et al.
Published: (2023-07-01)

NMT-GPT
by: Nina Kvalheim, et al.
Published: (2023-06-01)

Integrative single-cell RNA-seq analysis of vascularized cerebral organoids
by: Yuya Sato, et al.
Published: (2023-11-01)

scMGCN: A Multi-View Graph Convolutional Network for Cell Type Identification in scRNA-seq Data
by: Hongmin Sun, et al.
Published: (2024-02-01)

scEMAIL: Universal and Source-free Annotation Method for scRNA-seq Data with Novel Cell-type Perception
by: Hui Wan, et al.
Published: (2022-10-01)

scDA: Single cell discriminant analysis for single-cell RNA sequencing data
by: Qianqian Shi, et al.
Published: (2021-01-01)

Generation of Skin Organoids: Potential Opportunities and Challenges
by: Hui Sun, et al.
Published: (2021-11-01)

ScRNA-seq and bulk RNA-seq reveal the characteristics of ferroptosis and establish a risk signature in cholangiocarcinoma
by: Wenchao Yao, et al.
Published: (2022-12-01)

scDLC: a deep learning framework to classify large sample single-cell RNA-seq data
by: Yan Zhou, et al.
Published: (2022-07-01)

Choice of pre-processing pipeline influences clustering quality of scRNA-seq datasets
by: Inbal Shainer, et al.
Published: (2021-09-01)

Integration of scRNA-Seq and Bulk RNA-Seq Reveals Molecular Characterization of the Immune Microenvironment in Acute Pancreatitis
by: Zhen Fang, et al.
Published: (2022-12-01)

Organoids Are Limited in Modeling the Colon Adenoma–Carcinoma Sequence
by: Yoshihisa Tokumaru, et al.
Published: (2021-02-01)

Single-cell analysis reveals congruence between kidney organoids and human fetal kidney
by: Alexander N. Combes, et al.
Published: (2019-01-01)

Doublet identification in single-cell sequencing data using scDblFinder [version 2; peer review: 2 approved]
by: Aaron Lun, et al.
Published: (2022-05-01)

CellRegMap: a statistical framework for mapping context‐specific regulatory variants using scRNA‐seq
by: Anna S E Cuomo, et al.
Published: (2022-08-01)

Preservation of scRNA-Seq Libraries Using Existing Inactivation Protocols
by: Gail L. Sturdevant, et al.
Published: (2024-02-01)

NMT konferansen 2023
by: Thomas Gjesteland, et al.
Published: (2023-05-01)

Boosting scRNA-seq data clustering by cluster-aware feature weighting
by: Rui-Yi Li, et al.
Published: (2021-06-01)

scSID: A lightweight algorithm for identifying rare cell types by capturing differential expression from single-cell sequencing data
by: Shudong Wang, et al.
Published: (2024-12-01)

scRNA-seq reveals ATPIF1 activity in control of T cell antitumor activity
by: Genshen Zhong, et al.
Published: (2022-12-01)