e-learning

Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)

Abstract

This tutorial uses ChIP-seq datasets from a study published by. The goal of this study was to investigate "the dynamics of occupancy and the role in gene regulation of the transcription factor TAL1, a critical regulator of hematopoiesis, at multiple stages of hematopoietic differentiation."

About This Material

This is a Hands-on Tutorial from the GTN which is usable either for individual self-study, or as a teaching material in a classroom.

Questions this will address

  • How is raw ChIP-seq data processed and analyzed?
  • What are the binding sites of TAL1?
  • Which genes are regulated by TAL1?

Learning Objectives

  • Inspect read quality with FastQC
  • Perform read trimming with Trimmomatic
  • Align trimmed reads with BWA
  • Assess quality and reproducibility of experiments
  • Identify TAL1 binding sites with MACS2
  • Determine unique/common TAL1 binding sites from G1E and Megakaryocytes
  • Identify unique/common TAL1 peaks occupying gene promoters
  • Visually inspect TAL1 peaks with Trackster

Licence: Creative Commons Attribution 4.0 International

Keywords: ChIP-seq, Epigenetics

Target audience: Students

Resource type: e-learning

Version: 10

Status: Active

Prerequisites:

  • Introduction to Galaxy Analyses
  • Mapping
  • Quality Control
  • Trackster

Learning objectives:

  • Inspect read quality with FastQC
  • Perform read trimming with Trimmomatic
  • Align trimmed reads with BWA
  • Assess quality and reproducibility of experiments
  • Identify TAL1 binding sites with MACS2
  • Determine unique/common TAL1 binding sites from G1E and Megakaryocytes
  • Identify unique/common TAL1 peaks occupying gene promoters
  • Visually inspect TAL1 peaks with Trackster

Date modified: 2024-06-25

Date published: 2016-12-20

Authors: Anika Erxleben, Joachim Wolff, Mallory Freeberg, Mo Heydarian, Vivek Bhardwaj

Contributors: Björn Grüning, Bérénice Batut, Fidel Ramirez, Friederike Dündar, Helena Rasche, Mallory Freeberg, Maria Doyle, Niall Beard, Nicola Soranzo, Saskia Hiltemann, William Durand

Scientific topics: Epigenomics, ChIP-seq


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