Dataset Open Access
Vierstra, Jeff;
Stamatoyannopoulos, John A
Vierstra, J. et al. Global reference mapping of human transcription factor footprints. Nature 583, 729–736 (2020). https://doi.org/10.1038/s41586-020-2528-x
Preprint @ bioRxiv: https://doi.org/10.1101/2020.01.31.927798
Contact: Jeff Vierstra (jvierstra@altius.org)
Genomic DNase I footprinting enables quantitative, nucleotide-resolution delineation of sites of transcription factor occupancy within native chromatin. We combined sampling of >67 billion uniquely mapping DNase I cleavages from >240 human cell types and states to index, with unprecedented accuracy and resolution, human genomic footprints and thereby the sequence elements that encode transcription factor recognition sites.
Please see http://vierstra.org/resources/dgf for additional information and a complete set of raw DNase I data for individual datasets. Additionally, raw data can also be accessed via the ENCODE data portal (http://encodeproject.org) using the dataset accessions found in Supplementary Table 1.
Code for footprint analysis and tutorials on how to access and manipulate digital genomic footprint data can be found at https://footprint-tools.readthedocs.io/en/latest/.
All files herein correspond to human genome build version GRCh38 (UCSC hg38).
Dataset contents:
Name | Size | |
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collapsed_motifs_overlapping_consensus_footprints_hg38.bed.gz
md5:c9abbcb6eab93b7912c6a033325e66d1 |
427.6 MB | Download |
collapsed_motifs_overlapping_consensus_footprints_legend.txt
md5:971d028d1649dd7d7c4320f95fd54dd5 |
799 Bytes | Download |
consensus_footprints_and_motifs_hg38.bed.gz
md5:1ab941adcda42e7b54cd93da89dd9723 |
584.0 MB | Download |
consensus_footprints_and_motifs_legend.txt
md5:35adfcbdf0e4d4fb6b2a15e2ad6deee4 |
1.3 kB | Download |
consensus_index_matrix_binary_hg38.txt.gz
md5:15f3da13cd57217af1407e0271251ab6 |
65.5 MB | Download |
consensus_index_matrix_full_hg38.txt.gz
md5:099f7fc5a080afde2002646c8bfa3e7d |
1.4 GB | Download |
genotypes.vcf.gz
md5:52096331fbfec008a1a198f888e81ca5 |
354.8 MB | Download |
Supplementary_Table_1.xlsx
md5:920e1eee2547cef2c4f235ae8eaba3ff |
42.4 kB | Download |
Supplementary_Table_2.xlsx
md5:920e1eee2547cef2c4f235ae8eaba3ff |
42.4 kB | Download |
Supplementary_Table_3.xlsx
md5:920e1eee2547cef2c4f235ae8eaba3ff |
42.4 kB | Download |
tested_snvs_padj.bed.gz
md5:a8deccf73a5d4ee45bf03cfa8aed37de |
35.3 MB | Download |
tested_snvs_padj_legend.txt
md5:29db108b5dd59232e8e7ad3fa77d0634 |
899 Bytes | Download |
Vierstra et al. Global reference mapping and dynamics of human transcription factor footprints. (2020). bioRxiv
All versions | This version | |
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Data volume | 328.8 GB | 264.3 GB |
Unique views | 1,666 | 1,276 |
Unique downloads | 495 | 434 |