Stable nucleosomes of the human genome
Below is the database of regions with stable nucleosome occupancy in the human genome, calculated based on MNase-seq in B-cells and cell-free DNA in patients and healthy controls. This section is part of NucPosDB, a central nucleosome positioning database.
Jump to: NucPosDB front page | stable nucleosomes of the human genome | experimental nucleosome maps in vivo | experimental cfDNA datasets | tools for analysis of nucleosome mapping experiments | tools for prediction of nucleosome maps from DNA sequence | tools for analysis of sequenced cfDNA
How to cite: Shtumpf M., Piroeva K.V., Agrawal S.P., Jacob D.R., Teif V.B. (2022). NucPosDB: a database of nucleosome positioning in vivo and nucleosomics of cell-free DNA. Chromosoma 131, 19-28 | open access article
The stable-nucleosome regions provided below were reconstructed per-condition, based on the corresponding datasets of all mapped cfDNA fragments from Snyder et al 2016, Song et al 2017, Butler et al 2015 and Ma et al, 2017, as well as the high-resolution dataset of MNase-seq in lymphoblastoid B-cells from Gaffney et a., 2012. Per-condition datasets of stable nucleosomes are organised in these directories:
stable-nucleosome regions per-condition (hg38)
stable-nucleosome regions per-condition (hg19)
Below we provide the histograms of fragment size distribution for conditions where at least two datasets are reported by independent laboratories or where separate per-patient datasets are available. The datasets with all mapped DNA fragments can be found in the main cfDNA repository.
cfDNA in breast cancer:
cfDNA in lung cancer:
cfDNA in gastric cancer:
cfDNA in healthy people:
MNase-seq in healthy lymphoblastoid B-cells:
Jump to: NucPosDB front page | experimental nucleosome maps in vivo | experimental cfDNA datasets | tools for analysis of nucleosome mapping experiments | tools for prediction of nucleosome maps from DNA sequence | tools for analysis of sequenced cfDNA