Schema for MACS2 DHS - DNaseI Hypersensitive Sites Identified by MACS2

Database: dm6 Primary Table: uwstam_DNaseI_stage10_macs Row Count: 31,732 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	5471	`int(10) unsigned`	range
`chromEnd`	5968	`int(10) unsigned`	range
`name`	uwstam_DNaseI_stage10_macs_...	`varchar(255)`	values
`score`	81	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	2.92676	`float`	range
`pValue`	9.69942	`float`	range
`qValue`	8.12401	`float`	range
`peak`	130	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	5471	5968	uwstam_DNaseI_stage10_macs_peak_1a	81	.	2.92676	9.69942	8.12401	130
585	chr2L	5471	5968	uwstam_DNaseI_stage10_macs_peak_1b	2103	.	16.7022	213.081	210.345	324
585	chr2L	7466	7586	uwstam_DNaseI_stage10_macs_peak_2	87	.	2.84289	10.3532	8.76026	55
585	chr2L	12513	12709	uwstam_DNaseI_stage10_macs_peak_3	60	.	2.51016	7.52034	6.01475	161
585	chr2L	15203	15385	uwstam_DNaseI_stage10_macs_peak_4	81	.	2.66904	9.71977	8.14396	107
585	chr2L	17542	17820	uwstam_DNaseI_stage10_macs_peak_5a	260	.	4.09459	27.9214	26.0401	74
585	chr2L	17542	17820	uwstam_DNaseI_stage10_macs_peak_5b	146	.	3.20096	16.4179	14.6918	201
585	chr2L	18773	19024	uwstam_DNaseI_stage10_macs_peak_6	262	.	4.01116	28.1186	26.2354	138
585	chr2L	21610	22017	uwstam_DNaseI_stage10_macs_peak_7a	458	.	5.25356	47.8807	45.8268	171
585	chr2L	21610	22017	uwstam_DNaseI_stage10_macs_peak_7b	32	.	1.90246	4.57118	3.20568	332

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

MACS2 DHS (dhs_macs_std) Track Description

Description

These tracks show the positions of DNase I Hypersensitive Sites (DHS). The peak calls and the log likelihood ratio evidence tracks were produced by MACS2.

The DHS datasets were obtained from the Sequence Read Archive at NCBI under the following accession numbers:

Accession	Developmental Stages / Cell Lines	Reference
SRP010823	S2	Kharchenko PV et al., 2011
SRP005657	Kc167	Kharchenko PV et al., 2011
SRP002474	Embryonic Stages 5, 9, 10, 11, 14	Thomas S et al., 2011
SRP015758	S2, OSC	Arnold CD et al., 2013
SRP112733	Wild-type, Elav+, Mef2+ 6-8hr Embryonic Nuclei	Cusanovich DA et al., 2018

References

Kharchenko PV, Alekseyenko AA, Schwartz YB, Minoda A, Riddle NC, Ernst J, Sabo PJ, Larschan E, Gorchakov AA, Gu T, Linder-Basso D, Plachetka A, Shanower G, Tolstorukov MY, Luquette LJ, Xi R, Jung YL, Park RW, Bishop EP, Canfield TK, Sandstrom R, Thurman RE, MacAlpine DM, Stamatoyannopoulos JA, Kellis M, Elgin SC, Kuroda MI, Pirrotta V, Karpen GH, Park PJ. Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. Nature. 2011 Mar 24;471(7339):480-5.

Thomas S, Li XY, Sabo PJ, Sandstrom R, Thurman RE, Canfield TK, Giste E, Fisher W, Hammonds A, Celniker SE, Biggin MD, Stamatoyannopoulos JA. Dynamic reprogramming of chromatin accessibility during Drosophila embryo development. Genome Biol. 2011;12(5):R43.

Arnold CD, Gerlach D, Stelzer C, Boryń ŁM, Rath M, Stark A. Genome-wide quantitative enhancer activity maps identified by STARR-seq. Science. 2013 Mar 1;339(6123):1074-7.

Cusanovich DA, Reddington JP, Garfield DA, Daza RM, Aghamirzaie D, Marco-Ferreres R, Pliner HA, Christiansen L, Qiu X, Steemers FJ, Trapnell C, Shendure J, Furlong EEM. The cis-regulatory dynamics of embryonic development at single-cell resolution. Nature. 2018 Mar 22;555(7697):538-542.

Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137.