Schema for MACS2 DHS - DNaseI Hypersensitive Sites Identified by MACS2

Database: dm6 Primary Table: uwstam_DNaseI_stage14_macs Row Count: 21,970 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	16302	`int(10) unsigned`	range
`chromEnd`	16435	`int(10) unsigned`	range
`name`	uwstam_DNaseI_stage14_macs_...	`varchar(255)`	values
`score`	80	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	4.28302	`float`	range
`pValue`	10.0883	`float`	range
`qValue`	8.0916	`float`	range
`peak`	60	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	16302	16435	uwstam_DNaseI_stage14_macs_peak_1	80	.	4.28302	10.0883	8.0916	60
585	chr2L	18610	18689	uwstam_DNaseI_stage14_macs_peak_2	71	.	3.63023	9.1328	7.17295	39
585	chr2L	18844	19067	uwstam_DNaseI_stage14_macs_peak_3	287	.	7.22767	31.2941	28.7794	71
585	chr2L	19133	19275	uwstam_DNaseI_stage14_macs_peak_4	97	.	4.14508	11.7647	9.70707	89
585	chr2L	21669	21849	uwstam_DNaseI_stage14_macs_peak_5	873	.	14.8372	90.6511	87.3971	66
585	chr2L	35607	35818	uwstam_DNaseI_stage14_macs_peak_6a	41	.	3.11284	5.92662	4.12779	18
585	chr2L	35607	35818	uwstam_DNaseI_stage14_macs_peak_6b	71	.	3.89529	9.09726	7.13863	110
585	chr2L	42258	42378	uwstam_DNaseI_stage14_macs_peak_7	75	.	4.04989	9.4983	7.52514	63
585	chr2L	43227	43309	uwstam_DNaseI_stage14_macs_peak_8	31	.	2.90549	4.86518	3.14029	46
585	chr2L	59178	59505	uwstam_DNaseI_stage14_macs_peak_9a	138	.	5.51471	16.0147	13.8249	61

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.