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Amplification of pico-scale DNA mediated by bacterial carrier DNA for small-cell-number transcription factor ChIP-seq

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  1. Gene editing in the context of an increasingly complex genome

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  2. Strategy for efficient generation of numerous full-length cDNA clones of classical swine fever virus for haplotyping

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  3. A correction for sample overlap in genome-wide association studies in a polygenic pleiotropy-informed framework

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  4. Is genotyping of single isolates sufficient for population structure analysis of Pseudomonas aeruginosa in cystic fibrosis airways?

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  5. Erratum to: Liver transcriptomic networks reveal main biological processes associated with feed efficiency in beef cattle

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  1. The splicing factor RBM25 controls MYC activity in acute myeloid leukemia

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  2. BloodSpot: a database of healthy and malignant haematopoiesis updated with purified and single cell mRNA sequencing profiles

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  3. Genetic, Clinical, and Environmental Factors Associated With Persistent Atopic Dermatitis in Childhood

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  4. Leukemogenic nucleophosmin mutation disrupts the transcription factor hub regulating granulo-monocytic fates

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BackgroundChromatin-Immunoprecipitation coupled with deep sequencing (ChIP-seq) is used to map transcription factor occupancy and generate epigenetic profiles genome-wide. The requirement of nano-scale ChIP DNA for generation of sequencing libraries has impeded ChIP-seq on in vivo tissues of low cell numbers.ResultsWe describe a robust, simple and scalable methodology for ChIP-seq of low-abundant cell populations, verified down to 10,000 cells. By employing non-mammalian genome mapping bacterial carrier DNA during amplification, we reliably amplify down to 50 pg of ChIP DNA from transcription factor (CEBPA) and histone mark (H3K4me3) ChIP. We further demonstrate that genomic profiles are highly resilient to changes in carrier DNA to ChIP DNA ratios.ConclusionsThis represents a significant advance compared to existing technologies, which involve either complex steps of pre-selection for nucleosome-containing chromatin or pre-amplification of precipitated DNA, making them prone to introduce experimental biases.

Original languageEnglish
JournalB M C Genomics
Volume16
Issue number1
Pages (from-to)46
ISSN1471-2164
DOIs
Publication statusPublished - 5 Feb 2015

ID: 44975190