ArticleBMC genomics2015
Amplification of pico-scale DNA mediated by bacterial carrier DNA for small-cell-number transcription factor ChIP-seq.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 29 citations in OpenAlex.
- Distinct roles for NF-κB in hematopoietic stem cells and the bone marrow milieu in promoting hematopoietic aging.Cell reports · 2025Article
- The histone demethylase KDM5C functions as a tumor suppressor in AML by repression of bivalently marked immature genes.Leukemia · 2023Article
- Transcription factor-driven coordination of cell cycle exit and lineage-specification in vivo during granulocytic differentiation : In memoriam Professor Niels Borregaard.Nature communications · 2022Article
- nMOWChIP-seq: low-input genome-wide mapping of non-histone targets.NAR genomics and bioinformatics · 2022Article
- The AML-associated K313 mutation enhances C/EBPα activity by leading to C/EBPα overexpression.Cell death & disease · 2021Article
- ChIP-Sequencing of TET Proteins.Methods in molecular biology (Clifton, N.J.) · 2021Article
- μDamID: A Microfluidic Approach for Joint Imaging and Sequencing of Protein-DNA Interactions in Single Cells.Cell systems · 2020Article
- The KDM4/JMJD2 histone demethylases are required for hematopoietic stem cell maintenance.Blood · 2019Article
- Mutant CEBPA directly drives the expression of the targetable tumor-promoting factor CD73 in AML.Science advances · 2019Article
- High-throughput ChIPmentation: freely scalable, single day ChIPseq data generation from very low cell-numbers.BMC genomics · 2019Article
- Cell Type-Specific Survey of Epigenetic Modifications by Tandem Chromatin Immunoprecipitation Sequencing.Scientific reports · 2018Article
- PAtCh-Cap: input strategy for improving analysis of ChIP-exo data sets and beyond.Nucleic acids research · 2016Article
- Understanding the genetic liability to schizophrenia through the neuroepigenome.Schizophrenia research · 2016Review
- C/EBPα creates elite cells for iPSC reprogramming by upregulating Klf4 and increasing the levels of Lsd1 and Brd4.Nature cell biology · 2016Article
- A Microfluidic Device with Integrated Sonication and Immunoprecipitation for Sensitive Epigenetic Assays.Analytical chemistry · 2016Article
- Genome-wide epigenomic profiling for biomarker discovery.Clinical epigenetics · 2016Review
- cChIP-seq: a robust small-scale method for investigation of histone modifications.BMC genomics · 2015Article
- ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors.Nature methods · 2015Article
- A microfluidic device for epigenomic profiling using 100 cells.Nature methods · 2015Article
Corrections and comments
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Authors and funding
8 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.