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Chromatin Immunoprecipitation (ChIP) followed by microarray hybridization on the whole genome tiling arrays (ChIP-chip; Iyer et al., 2001; Ren et al., 2000) or followed by massively parallel DNA sequencing (ChIP-seq) (Johnson et al., 2007), are now established as powerful methods to identify all of the genomic regions bound by a protein of interest in a given condition (Keles, 2007).
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We have mapped SALL4 global gene targets using chromatin-immunoprecipitation followed by microarray hybridization (ChIP-on-chip) in myeloid leukemic NB4 cells [28], normal human CD34+ bone marrow cells, and 293 cells (unpublished data).
To determine the molecular mechanism(s) of SALL4 in normal hematopoiesis, leukemogenesis and ESC development, we have mapped SALL4 global gene targets using chromatin-immunoprecipitation followed by microarray hybridization (ChIP-on-chip) in normal human CD34+ bone marrow cells, myeloid leukemic NB4 cells and human ESCs.
We have mapped SALL4 global gene targets using chromatin-immunoprecipitation followed by microarray hybridization (ChIP-on-chip) in three types of cells that are related to SALL4 biological functions: leukemic cells [42], ESCs, and primary normal CD34+ cells (unpublished data), which have been correlated with the expression of these gene targets.
The samples were analyzed by microarray hybridization and quantitative PCR.
Labelling and microarray hybridization on 385K RefSeq mouse promoter arrays were performed by Source BioScience imaGenes (Berlin, Germany).
In total we performed 10 microarray hybridizations on males and 8 on females.
Data based on genomics, microarray hybridization results, and validated by polymerase chain reaction and slot blot DNA hybridizations.
Subsequent gene selections were based on microarray hybridization scores, proceeding from most abundant to least abundant.
Comparing expression profiles contained in both analyses performed on identical total RNA, we found that the expression profiles assessed by qRT-PCR or microarray hybridization were highly similar.
Each condition was probed by three microarray hybridizations.
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