Neph 2012, DNaseI Digital Genomic Footprinting from ENCODE/University of Washington.

This experiment, produced as part of the ENCODE Project, contains deep sequencing DNase data that will be used to identify sites where regulatory factors bind to the genome (footprints).
Footprinting is a technique used to define the DNA sequences that interact with and bind DNA-binding proteins, such as transcription factors, zinc-finger proteins, hormone-receptor complexes, and other chromatin-modulating factors like CTCF. The technique depends upon the strength and tight nature of protein-DNA interactions. In their native chromatin state, DNA sequences that interact directly with DNA-binding proteins are relatively protected from DNA-degrading endonucleases, while the exposed/unbound portions are readily degraded by such endonucleases. A massively parallel next-generation sequencing technique to define the DNase hypersensitive sites in the genome was adopted. The DNase samples were sequenced using next-generation sequencing machines to significantly higher depths of 300-fold or greater. This produces a base-pair level resolution of the DNase susceptibility maps of the native chromatin state. These base-pair resolution maps represent and are dependent upon the nature and the specificity of interaction of the DNA with the regulatory/modulatory proteins binding at specific loci in the genome; thus they represent the native chromatin state of the genome under investigation. The deep sequencing approach has been used to define the footprint landscape of the genome by identifying DNA motifs that interact with known or novel DNA-binding proteins.

• Raw data was downloaded from: UCSC
• Input file format: BAM
• Download date: 26-9-2016

From H. sapiens (Feb 2009 GRCh37/hg19).

DNase FAIRE data:

	Filename	Description	Feature	GEO-ID
1	wgEncodeUwDgfA549Aln.sga	DNaseI DGF - A549	DNaseI	-
2	wgEncodeUwDgfAg10803Aln.sga	DNaseI DGF - AG10803	DNaseI	-
3	wgEncodeUwDgfAoafAln.sga	DNaseI DGF - AoAF	DNaseI	-
4	wgEncodeUwDgfCd20ro01778Aln.sga	DNaseI DGF - CD20+_RO01778	DNaseI	-
5	wgEncodeUwDgfCd4naivewb11970640Aln.sga	DNaseI DGF - CD4+_Naive_Wb11970640	DNaseI	-
6	wgEncodeUwDgfGm06990Aln.sga	DNaseI DGF - GM06990	DNaseI	-
7	wgEncodeUwDgfGm12865Aln.sga	DNaseI DGF - GM12865	DNaseI	-
8	wgEncodeUwDgfH7esAln.sga	DNaseI DGF - H7-hESC	DNaseI	-
9	wgEncodeUwDgfHaeAln.sga	DNaseI DGF - HAEpiC	DNaseI	-
10	wgEncodeUwDgfHahAln.sga	DNaseI DGF - HA-h	DNaseI	-
11	wgEncodeUwDgfHaspAln.sga	DNaseI DGF - HA-sp	DNaseI	-
12	wgEncodeUwDgfHcfAln.sga	DNaseI DGF - HCF	DNaseI	-
13	wgEncodeUwDgfHcfaaAln.sga	DNaseI DGF - HCFaa	DNaseI	-
14	wgEncodeUwDgfHcmAln.sga	DNaseI DGF - HCM	DNaseI	-
15	wgEncodeUwDgfHcpeAln.sga	DNaseI DGF - HCPEpiC	DNaseI	-
16	wgEncodeUwDgfHeeAln.sga	DNaseI DGF - HEEpiC	DNaseI	-
17	wgEncodeUwDgfHepg2Aln.sga	DNaseI DGF - HepG2	DNaseI	-
18	wgEncodeUwDgfHffAln.sga	DNaseI DGF - HFF	DNaseI	-
19	wgEncodeUwDgfHgfAln.sga	DNaseI DGF - HGF	DNaseI	-
20	wgEncodeUwDgfHipeAln.sga	DNaseI DGF - HIPEpiC	DNaseI	-
21	wgEncodeUwDgfHmfAln.sga	DNaseI DGF - HMF	DNaseI	-
22	wgEncodeUwDgfHmvecbAln.sga	DNaseI DGF - HMVEC-LLy	DNaseI	-
23	wgEncodeUwDgfHmvecdAln.sga	DNaseI DGF - HMVEC-dBl-Neo	DNaseI	-
24	wgEncodeUwDgfHmvecdbladAln.sga	DNaseI DGF - HMVEC-dBl-Ad	DNaseI	-
25	wgEncodeUwDgfHmvecfAln.sga	DNaseI DGF - HMVEC-dLy-Neo	DNaseI	-
26	wgEncodeUwDgfHmvechAln.sga	DNaseI DGF - HMVEC-LBl	DNaseI	-
27	wgEncodeUwDgfHpafAln.sga	DNaseI DGF - HPAF	DNaseI	-
28	wgEncodeUwDgfHpdlfAln.sga	DNaseI DGF - HPdLF	DNaseI	-
29	wgEncodeUwDgfHpfAln.sga	DNaseI DGF - HPF	DNaseI	-
30	wgEncodeUwDgfHrceAln.sga	DNaseI DGF - HRCEpiC	DNaseI	-
31	wgEncodeUwDgfHsmmAln.sga	DNaseI DGF - HSMM	DNaseI	-
32	wgEncodeUwDgfHuvecAln.sga	DNaseI DGF - HUVEC	DNaseI	-
33	wgEncodeUwDgfHvmfAln.sga	DNaseI DGF - HVMF	DNaseI	-
34	wgEncodeUwDgfK562Aln.sga	DNaseI DGF - K562 rep1	DNaseI	-
35	wgEncodeUwDgfK562Znfa41c6Aln.sga	DNaseI DGF - K562 rep2	DNaseI	-
36	wgEncodeUwDgfK562Znfp5Aln.sga	DNaseI DGF - K562 rep3	DNaseI	-
37	wgEncodeUwDgfLhcnm2Aln.sga	DNaseI DGF - LHCN-M2 rep1	DNaseI	-
38	wgEncodeUwDgfLhcnm2Diff4dAln.sga	DNaseI DGF - LHCN-M2 rep2	DNaseI	-
39	wgEncodeUwDgfM059jAln.sga	DNaseI DGF - M059J	DNaseI	-
40	wgEncodeUwDgfMonocd14ro1746Aln.sga	DNaseI DGF - Monocytes-CD14+_RO01746	DNaseI	-
41	wgEncodeUwDgfNb4Aln.sga	DNaseI DGF - NB4	DNaseI	-
42	wgEncodeUwDgfNhaAln.sga	DNaseI DGF - NH-A	DNaseI	-
43	wgEncodeUwDgfNhdfadAln.sga	DNaseI DGF - NHDF-Ad	DNaseI	-
44	wgEncodeUwDgfNhdfneoAln.sga	DNaseI DGF - NHDF-neo	DNaseI	-
45	wgEncodeUwDgfNhlfAln.sga	DNaseI DGF - NHLF	DNaseI	-
46	wgEncodeUwDgfRpmi7951Aln.sga	DNaseI DGF - RPMI-7951	DNaseI	-
47	wgEncodeUwDgfSaecAln.sga	DNaseI DGF - SAEC	DNaseI	-
48	wgEncodeUwDgfSkmcAln.sga	DNaseI DGF - SKMC	DNaseI	-
49	wgEncodeUwDgfSknshraAln.sga	DNaseI DGF - SK-N-SH_RA	DNaseI	-
50	wgEncodeUwDgfT47dAln.sga	DNaseI DGF - T-47D	DNaseI	-
51	wgEncodeUwDgfTh17Aln.sga	DNaseI DGF - Th17	DNaseI	-
52	wgEncodeUwDgfTh1Aln.sga	DNaseI DGF - Th1	DNaseI	-
53	wgEncodeUwDgfTh1AlnRep2.sga	DNaseI DGF - Th1	DNaseI	-
54	wgEncodeUwDgfTh1wb33676984Aln.sga	DNaseI DGF - Th1_Wb33676984	DNaseI	-
55	wgEncodeUwDgfTh2Aln.sga	DNaseI DGF - Th2	DNaseI	-
56	wgEncodeUwDgfTh2wb54553204Aln.sga	DNaseI DGF - Th2_Wb54553204	DNaseI	-
57	wgEncodeUwDgfTregwb78495824Aln.sga	DNaseI DGF - Treg_Wb78495824	DNaseI	-

BAM files were converted to bed using bamToBed v2.12.0 (bedtools). SGA conversion was carried out using bed2sga.pl (ChIP-Seq v. 1.5.3).

• Neph S, Vierstra J, Stergachis AB, Reynolds AP, Haugen E, Vernot B, Thurman RE, John S, Sandstrom R, Johnson AK, Maurano MT, Humbert R, Rynes E, Wang H, Vong S, Lee K, Bates D, Diegel M, Roach V, Dunn D, Neri J, Schafer A, Hansen RS, Kutyavin T, Giste E, Weaver M, Canfield T, Sabo P, Zhang M, Balasundaram G, Byron R, MacCoss MJ, Akey JM, Bender MA, Groudine M, Kaul R, Stamatoyannopoulos JA
  An expansive human regulatory lexicon encoded in transcription factor footprints. Nature. 2012 Sep 6;489(7414):83-90. doi: 10.1038/nature11212. 22955618
• GEO series GSE26328: DNaseI Digital Genomic Footprinting from ENCODE/University of Washington [Human]