Schema for MACS2 DHS - DNaseI Hypersensitive Sites Identified by MACS2

Database: dm6 Primary Table: uwstam_DNaseI_S2_macs Row Count: 38,473 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	5688	`int(10) unsigned`	range
`chromEnd`	5982	`int(10) unsigned`	range
`name`	uwstam_DNaseI_S2_macs_peak_1a	`varchar(255)`	values
`score`	237	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	4.80483	`float`	range
`pValue`	25.9226	`float`	range
`qValue`	23.7043	`float`	range
`peak`	104	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	5688	5982	uwstam_DNaseI_S2_macs_peak_1a	237	.	4.80483	25.9226	23.7043	104
585	chr2L	5688	5982	uwstam_DNaseI_S2_macs_peak_1b	157	.	3.95692	17.7863	15.7087	224
585	chr2L	18854	18945	uwstam_DNaseI_S2_macs_peak_2	182	.	4.23956	20.3869	18.2604	48
585	chr2L	21709	21769	uwstam_DNaseI_S2_macs_peak_3	83	.	3.03835	10.2234	8.33312	29
585	chr2L	28015	28140	uwstam_DNaseI_S2_macs_peak_4	21	.	1.97846	3.61025	2.15902	40
585	chr2L	46030	46200	uwstam_DNaseI_S2_macs_peak_5	50	.	2.54373	6.81084	5.06164	51
585	chr2L	46637	46744	uwstam_DNaseI_S2_macs_peak_6	50	.	2.54373	6.81084	5.06164	61
585	chr2L	46828	46975	uwstam_DNaseI_S2_macs_peak_7a	83	.	3.03835	10.2234	8.33312	37
585	chr2L	46828	46975	uwstam_DNaseI_S2_macs_peak_7b	78	.	2.96769	9.70473	7.83159	110
585	chr2L	47194	47446	uwstam_DNaseI_S2_macs_peak_8a	93	.	3.17967	11.2897	9.36681	28

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.