Schema for MACS2 DHS - DNaseI Hypersensitive Sites Identified by MACS2

Database: dm6 Primary Table: GSE101581_DNaseI_Elav_macs Row Count: 27,803 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	5204	`int(10) unsigned`	range
`chromEnd`	5968	`int(10) unsigned`	range
`name`	GSE101581_DNaseI_Elav_macs_...	`varchar(255)`	values
`score`	41	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	1.72688	`float`	range
`pValue`	5.39922	`float`	range
`qValue`	4.10953	`float`	range
`peak`	264	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	5204	5968	GSE101581_DNaseI_Elav_macs_peak_1b	41	.	1.72688	5.39922	4.10953	264
585	chr2L	5204	5968	GSE101581_DNaseI_Elav_macs_peak_1c	619	.	4.46687	63.6743	61.9304	568
585	chr2L	5204	5968	GSE101581_DNaseI_Elav_macs_peak_1a	71	.	1.98016	8.54486	7.19446	71
585	chr2L	6649	6784	GSE101581_DNaseI_Elav_macs_peak_2	146	.	2.46369	16.1391	14.6931	67
585	chr2L	7680	7844	GSE101581_DNaseI_Elav_macs_peak_3	20	.	1.51966	3.31675	2.08584	35
585	chr2L	8330	8492	GSE101581_DNaseI_Elav_macs_peak_4	46	.	1.77293	5.92401	4.62256	44
585	chr2L	8874	9122	GSE101581_DNaseI_Elav_macs_peak_5	31	.	1.63478	4.41605	3.15108	96
585	chr2L	18153	19273	GSE101581_DNaseI_Elav_macs_peak_6a	1179	.	4.33158	119.847	117.901	158
585	chr2L	18153	19273	GSE101581_DNaseI_Elav_macs_peak_6b	11929	.	16.4354	1196.33	1192.97	476
585	chr2L	18153	19273	GSE101581_DNaseI_Elav_macs_peak_6c	3013	.	7.04135	303.649	301.302	657

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.