Stem Cell Transcriptional Networks Methods and Protocols [Hardcover]

Stem Cell Transcriptional Networks: Methods and Protocols collects techniques used to increase our understanding of the underlying transcriptional programs of stem cells that promote self-renewal and differentiation. The volume opens with a section on next-generation sequencing library preparation and data analysis. Continuing with a collection of protocols on visual analysis and interpretation of large-scale interaction networks, this detailed compilation features transcriptional networks in embryonic and adult stem cells, embryo culture and derivation of stem cells, as well as transcriptional programs that promote self-renewal, reprogramming, and transdifferentiation. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials, step-by-step, readily reproducible protocols and tips on troubleshooting and avoiding known pitfalls.

Authoritative and practical, Stem Cell Transcriptional Networks: Methods and Protocols aims to provide a key resource for biologists seeking to interrogate these vital networks.

Part I: Next-Generation Sequencing Library Preparation and Data Analysis

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1. Efficient Library Preparation for Next-Generation Sequencing Analysis of Genome-Wide Epigenetic and Transcriptional Landscapes in Embryonic Stem Cells

??????????? Benjamin L. Kidder and Keji Zhao

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2. Analysis of Next-Generation Sequencing Data Using Galaxy

??????????? Daniel Blankenberg and Jennifer Hillman-Jackson

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3. edgeR for Differential RNA-seq? and ChIP-seq Analysis: An Application? to Stem? Cell Biology

??????????? Olga Nikolayeva and Mark D. Robinson

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4. Use Model-lr