ArticleBMC genomics2012
Limitations and possibilities of low cell number ChIP-seq.
Article in BMC genomics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed.
- Epigenetic Analysis in Ewing Sarcoma.Methods in molecular biology (Clifton, N.J.) · 2027Article
- CUT&RUN as a Powerful Tool for Chromatin Profiling: A Focus on Neuropsychiatric Disorders.Biological psychiatry · 2026Review
- Methods for Investigating the Sperm Epigenome.Advances in experimental medicine and biology · 2026Review
- Writing the Engram: Epigenetic Mechanisms of Memory Allocation.Journal of neurochemistry · 2025Review
- ChIP-mini: a low-input ChIP-exo protocol for elucidating DNA-binding protein dynamics in intracellular pathogens.Nucleic acids research · 2025Article
- Article
- Analysis of super-enhancer using machine learning and its application to medical biology.Briefings in bioinformatics · 2023Review
- 2cChIP-seq and 2cMeDIP-seq: The Carrier-Assisted Methods for Epigenomic Profiling of Small Cell Numbers or Single Cells.International journal of molecular sciences · 2022Article
- Commercial ChIP-Seq Library Preparation Kits Performed Differently for Different Classes of Protein Targets.Journal of biomolecular techniques : JBT · 2022Article
- Cell division in the shoot apical meristem is a trigger for miR156 decline and vegetative phase transition inProceedings of the National Academy of Sciences of the United States of America · 2021Article
- Integrative analysis of epigenetics data identifies gene-specific regulatory elements.Nucleic acids research · 2021Article
- To mock or not: a comprehensive comparison of mock IP and DNA input for ChIP-seq.Nucleic acids research · 2021Article
- Self-organizing maps with variable neighborhoods facilitate learning of chromatin accessibility signal shapes associated with regulatory elements.BMC bioinformatics · 2021Article
- EpiRegio: analysis and retrieval of regulatory elements linked to genes.Nucleic acids research · 2020Article
- Profiling chromatin regulatory landscape: insights into the development of ChIP-seq and ATAC-seq.Molecular biomedicine · 2020Review
- Pinpointing the Genomic Localizations of Chromatin-Associated Proteins: The Yesterday, Today, and Tomorrow of ChIP-seq.Current protocols in cell biology · 2019Article
- [The improvewment of DNA library construction in non-crosslinked chromatin immunoprecipitation coupled with next-generation sequencing].Nan fang yi ke da xue xue bao = Journal of Southern Medical University · 2019Article
- Approaches for the study of epigenetic modifications in the inner ear and related tissues.Hearing research · 2019Review
- An inhibitor screen identifies histone-modifying enzymes as mediators of polymer-mediated transgene expression from plasmid DNA.Journal of controlled release : official journal of the Controlled Release Society · 2018Article
- An optimized FAIRE procedure for low cell numbers in yeast.Yeast (Chichester, England) · 2018Article
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundChromatin immunoprecipitation coupled with high-throughput DNA sequencing (ChIP-seq) offers high resolution, genome-wide analysis of DNA-protein interactions. However, current standard methods require abundant starting material in the range of 1-20 million cells per immunoprecipitation, and remain a bottleneck to the acquisition of biologically relevant epigenetic data. Using a ChIP-seq protocol optimised for low cell numbers (down to 100,000 cells/IP), we examined the performance of the ChIP-seq technique on a series of decreasing cell numbers.
resultsWe present an enhanced native ChIP-seq method tailored to low cell numbers that represents a 200-fold reduction in input requirements over existing protocols. The protocol was tested over a range of starting cell numbers covering three orders of magnitude, enabling determination of the lower limit of the technique. At low input cell numbers, increased levels of unmapped and duplicate reads reduce the number of unique reads generated, and can drive up sequencing costs and affect sensitivity if ChIP is attempted from too few cells.
conclusionsThe optimised method presented here considerably reduces the input requirements for performing native ChIP-seq. It extends the applicability of the technique to isolated primary cells and rare cell populations (e.g. biobank samples, stem cells), and in many cases will alleviate the need for cell culture and any associated alteration of epigenetic marks. However, this study highlights a challenge inherent to ChIP-seq from low cell numbers: as cell input numbers fall, levels of unmapped sequence reads and PCR-generated duplicate reads rise. We discuss a number of solutions to overcome the effects of reducing cell number that may aid further improvements to ChIP performance.
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