ChIP-Sequencing（ChIP-Seq）服务

Generating data is only half the battle in ChIP-Seq. When the sequencing is complete, tens of millions of short sequence tags must be mapped back to the genome followed by peak calling. Peak calling is complicated by the fact that different algorithms are required for accurate peak calling depending on the antibody used. Thousands to tens of thousands of binding sites must then be exported into a meaningful output that relates the data to genes and allows for multiple samples to be compared to one another. Challenges continue with clustering, heat maps and graphical representations of genome-wide localization patterns. This type of in-depth bioinformatics analysis is beyond the capabilities of most labs. That is why data analysis is part of the standard package for all of our ChIP-Seq Service projects.

Figure 3: Compilation of all genomic binding sites relative to gene transcription start sites (TSS). ChIP-Seq was performed with antibodies against the histone demethylase KDM1A and one of its targets, Histone H3 dimethyl Lys4 (H3K4me2). Thousands of binding sites were identified and the positions of all binding sites, as they relate to gene annotations, were compiled. Left. A heat map was created using all genes bound by H3K4me2 and KDM1A and the occupancy of these factors around the transcription start site (TSS) is depicted. Top. The same data depicted a different way shows KDM1A occupancy between the two peaks of H3K4me2 occupancy.

The selected papers below cite the use of and/or provide additional information about ChIP-Seq Services provided by Active Motif’s Epigenetic Services:

“Reduced H3K27me3 and DNA Hypomethylation Are Major Drivers of Gene Expression in K27M Mutant Pediatric High-Grade Gliomas” by Bender et al (2013) Cancer Cell 24(5):660-672.
“Atrial Identity Is Determined by a COUP-TFII Regulatory Network” by Wu et al (2013) Developmental Cell 25(4):417-426.
“Specification of type 2 innate lymphocytes by the transcriptional determinant Gfi1” by Spooner et al (2013) Nature Immunology 14(2):1229-1236.
“EZH2 inhibition as a therapeutic strategy for lymphoma with EZH2-activating mutations” by McCabe et al (2012) Nature 492(7427):108-112.
“Loss of the Tumor Suppressor BAP1 Causes Myeloid Transformation” by Dey et al (2012) Science 337(6101):1541-1546.
“ChIP sequencing of cyclin D1 reveals a transcriptional role in chromosomal instability in mice” by Casimiro et al (2011) Journal of Clinical Investigation 122(3):833-843.
“Global Characterization of Transcriptional Impact of the SRC-3 Coregulator” by Lanz et al (2010) Molecular Endocrinology 24(4):859-872.
“A ChIP-seq defined genome-wide map of vitamin D receptor binding: Associations with disease and evolution” by Ramagopalan et al (2010) Genome Research 20(10):1352-1360.
“miR-155 Inhibition Sensitizes CD4+ Th Cells for TREG Mediated Suppression” by Stahl et al (2009) PLoS ONE 4(9):e7158.