Schema for MACS2 DHS - DNaseI Hypersensitive Sites Identified by MACS2

Database: dm6 Primary Table: GSE40739_DNaseI_S2_macs Row Count: 11,963 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	5617	`int(10) unsigned`	range
`chromEnd`	6001	`int(10) unsigned`	range
`name`	GSE40739_DNaseI_S2_macs_peak_1	`varchar(255)`	values
`score`	195	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	5.52819	`float`	range
`pValue`	21.9316	`float`	range
`qValue`	19.5603	`float`	range
`peak`	242	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	5617	6001	GSE40739_DNaseI_S2_macs_peak_1	195	.	5.52819	21.9316	19.5603	242
585	chr2L	18589	18849	GSE40739_DNaseI_S2_macs_peak_2a	66	.	3.61191	8.5616	6.60394	58
585	chr2L	18589	18849	GSE40739_DNaseI_S2_macs_peak_2b	50	.	3.17211	6.96909	5.09077	197
585	chr2L	66749	67402	GSE40739_DNaseI_S2_macs_peak_3a	783	.	9.36603	81.6022	78.3481	171
585	chr2L	66749	67402	GSE40739_DNaseI_S2_macs_peak_3b	130	.	4.2079	15.2704	13.0698	583
585	chr2L	71618	71775	GSE40739_DNaseI_S2_macs_peak_4	57	.	2.98866	7.63695	5.72217	76
585	chr2L	72015	72821	GSE40739_DNaseI_S2_macs_peak_5a	362	.	6.86404	38.99	36.296	187
585	chr2L	72015	72821	GSE40739_DNaseI_S2_macs_peak_5b	431	.	7.16919	45.965	43.1626	311
585	chr2L	72015	72821	GSE40739_DNaseI_S2_macs_peak_5c	611	.	7.55152	64.1514	61.1005	476
585	chr2L	72865	73561	GSE40739_DNaseI_S2_macs_peak_6	1827	.	16.8212	186.601	182.794	389

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.