ChIP-chip versus ChIP-seq: lessons for experimental design and data analysis (BMC Genomics. 2011 Feb 28;12:134)
ChIP-chip versus ChIP-seq: lessons for experimental design and data analysis.
Ho JW, Bishop E, Karchenko PV, Nègre N, White KP, Park PJ.
SourceDepartment of Medicine, Brigham and Women’s Hospital, and Harvard Medical School, Boston, MA, USA.
BACKGROUND: Chromatin immunoprecipitation (ChIP) followed by microarray hybridization (ChIP-chip) or high-throughput sequencing (ChIP-seq) allows genome-wide discovery of protein-DNA interactions such as transcription factor bindings and histone modifications. Previous reports only compared a small number of profiles, and little has been done to compare histone modification profiles generated by the two technologies or to assess the impact of input DNA libraries in ChIP-seq analysis. Here, we performed a systematic analysis of a modENCODE dataset consisting of 31 pairs of ChIP-chip/ChIP-seq profiles of the coactivator CBP, RNA polymerase II (RNA PolII), and six histone modifications across four developmental stages of Drosophila melanogaster.
RESULTS: Both technologies produce highly reproducible profiles within each platform, ChIP-seq generally produces profiles with a better signal-to-noise ratio, and allows detection of more peaks and narrower peaks. The set of peaks identified by the two technologies can be significantly different, but the extent to which they differ varies depending on the factor and the analysis algorithm. Importantly, we found that there is a significant variation among multiple sequencing profiles of input DNA libraries and that this variation most likely arises from both differences in experimental condition and sequencing depth. We further show that using an inappropriate input DNA profile can impact the average signal profiles around genomic features and peak calling results, highlighting the importance of having high quality input DNA data for normalization in ChIP-seq analysis.
CONCLUSIONS: Our findings highlight the biases present in each of the platforms, show the variability that can arise from both technology and analysis methods, and emphasize the importance of obtaining high quality and deeply sequenced input DNA libraries for ChIP-seq analysis.
- Protein quantitative trait loci identify novel candidates modulating cellular response to chemotherapy.
- Ancestral resurrection of the Drosophila S2E enhancer reveals accessible evolutionary paths through compensatory change.
- SPOP promotes tumorigenesis by acting as a key regulatory hub in kidney cancer.
- Defining functional DNA elements in the human genome.
- Low grade prostate cancer diverges early from high grade and metastatic disease.
- The spectrum of somatic mutations in high-risk acute myeloid leukaemia with -7/del(7q).
- Evolution of H3K27me3-marked chromatin is linked to gene expression evolution and to patterns of gene duplication and diversification.
- Diverse patterns of genomic targeting by transcriptional regulators in Drosophila melanogaster.
- Polarization of the effects of autoimmune and neurodegenerative risk alleles in leukocytes.
- CD33: increased inclusion of exon 2 implicates the Ig V-set domain in Alzheimer's disease susceptibility.