As example we will use data from ” Haseman et al. C/EBPα Is Required for Long-Term Self-Renewal and Lineage Priming of Hematopoietic Stem Cells and for the Maintenance of Epigenetic Configurations in Multipotent Progenitors. PLoS Genetic DOI: 10.1371/journal.pgen.1004079. “
In the immune system, myeloid cells arise from the hierarchical differentiation of hematopoietic stem cells (called LSK cells) into granulocyte-monocyte progenitors (GMP), which can give definitive differentiated cells (macrophages and granulocytes). The transcription factor CEBPa is a master regulator of myeloid differentiation, and its lost-of-function entails a block of differentiation before the GMP stage and is implied in accute myeloid leukemia.
In this paper, Haseman et al. performed a ChIP-seq analysis targeting CEBPa in LSK cells and GMP, in order to identify its targets in both cells types. They also performed ChIP-seq targeting histone marks characteristics of active enhancers (H3K4me3) and repressed ones (H3K27me3), in wild-type (WT) and Cebpa knock-out (KO) LSK cells, to identify the effect of CEBPa loss-of-function on enhancers activity.
We will use the CEBPa ChIP-seq in GMP (and control sample) as example for data pre-processing (quality controls, read mapping, peak calling and motif analysis).