Amplification of pico-scale DNA mediated by bacterial carrier DNA for small-cell-number transcription factor ChIP-seq
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Amplification of pico-scale DNA mediated by bacterial carrier DNA for small-cell-number transcription factor ChIP-seq. / Jakobsen, Janus S; Bagger, Frederik O; Hasemann, Marie S; Schuster, Mikkel B; Frank, Anne-Katrine; Waage, Johannes; Vitting-Seerup, Kristoffer; Porse, Bo Torben.
In: BMC Genomics, Vol. 16, 2015, p. 46.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Amplification of pico-scale DNA mediated by bacterial carrier DNA for small-cell-number transcription factor ChIP-seq
AU - Jakobsen, Janus S
AU - Bagger, Frederik O
AU - Hasemann, Marie S
AU - Schuster, Mikkel B
AU - Frank, Anne-Katrine
AU - Waage, Johannes
AU - Vitting-Seerup, Kristoffer
AU - Porse, Bo Torben
PY - 2015
Y1 - 2015
N2 - BACKGROUND: Chromatin-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.RESULTS: We 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.CONCLUSIONS: This 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.
AB - BACKGROUND: Chromatin-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.RESULTS: We 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.CONCLUSIONS: This 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.
U2 - 10.1186/s12864-014-1195-4
DO - 10.1186/s12864-014-1195-4
M3 - Journal article
C2 - 25652644
VL - 16
SP - 46
JO - BMC Genomics
JF - BMC Genomics
SN - 1471-2164
ER -
ID: 136757616