This second edition provides techniques used to study of the underlying transcriptional programs of stem cells that promote self-renewal and differentiation. Chapters detail next-generation sequencing technologies, data analysis, protocols on analysis and visualization of single-cell RNA-Seq data, analysis of 3D chromatin architecture, interpretation of large-scale interaction networks, transcriptional networks in embryonic and adult stem cells, derivation of stem cells, and transcriptional programs that promote reprogramming, transdifferentiation, and cancer formation. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Authoritative and cutting-edge, Stem Cell Transcriptional Network: Methods and Protocols, Second Edition aims to provide a key resource for biologists seeking to interrogate these vital networks.

includes cutting-edge methods and protocols Provides step-by-step detail essential for reproducible results Contains key notes and implementation advice from the experts

Inhalt

Epitope Tagging ChIP-seq of DNA Binding Proteins using CETCh-seq.- User-friendly and Interactive Analysis of ChIP-seq data using EaSeq.- Evaluation of 3D Chromatin Interactions using Hi-C.- MSTD for Detecting Topological Domains from 3D Genomic Maps.- Creating 2D Occupancy Plots using plot2DO.- Detection of Epigenetic Field Defects Using a Weighted Epigenetic Distance-based Method.- Profiling Cell Type Abundance and Expression in Bulk Tissues with CIBERSORTx.- Visualization of Single Cell RNA-Seq Data using t-SNE in R.- Use of SuperCT for Enhanced Characterization of Single-cell Transcriptomic Profiles.- Interactive Alternative Splicing Analysis of Human Stem Cells using psichomics.- Gene Ontology Semantic Similarity Analysis using GOSemSim.- Derivation of Maternogenic Epiblast Stem Cells from Haploid Embryos.- Derivation of LIF-independent Embryonic Stem Cells using Inducible OCT4 Expression.- Simultaneous Derivation of Embryonic and Trophoblast Stem Cells from Mouse Blastocysts.- Reprogramming Fibroblasts to Neural Stem Cells by Overexpression of the Transcription factor Ptf1a.- Reprogramming of Fibroblasts to Neural Stem Cells by a Chemical Cocktail.- Efficient RNA-based Reprogramming of Disease-associated Primary Human Fibroblasts into Induced Pluripotent Stem Cells.- Direct Reprogramming Of Mouse Embryonic Fibroblasts to Induced Trophoblast Stem (iTS) Cells.- Characterization of Arsenic-induced Cancer Stem-like Cells.