Schema for MACS2 DHS - DNaseI Hypersensitive Sites Identified by MACS2

Database: dm6 Primary Table: GSE101581_DNaseI_embryos_macs Row Count: 24,384 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	5596	`int(10) unsigned`	range
`chromEnd`	6011	`int(10) unsigned`	range
`name`	GSE101581_DNaseI_embryos_ma...	`varchar(255)`	values
`score`	971	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	5.34868	`float`	range
`pValue`	99.0912	`float`	range
`qValue`	97.1379	`float`	range
`peak`	276	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	5596	6011	GSE101581_DNaseI_embryos_macs_peak_1	971	.	5.34868	99.0912	97.1379	276
585	chr2L	6654	6781	GSE101581_DNaseI_embryos_macs_peak_2	93	.	2.07655	10.7312	9.31575	54
585	chr2L	18177	19277	GSE101581_DNaseI_embryos_macs_peak_3a	1304	.	4.59723	132.561	130.492	145
585	chr2L	18177	19277	GSE101581_DNaseI_embryos_macs_peak_3b	10814	.	15.6402	1085.15	1081.47	453
585	chr2L	18177	19277	GSE101581_DNaseI_embryos_macs_peak_3c	3916	.	8.29912	394.339	391.648	600
585	chr2L	18177	19277	GSE101581_DNaseI_embryos_macs_peak_3d	890	.	3.83993	90.9241	89.0024	835
585	chr2L	20469	20737	GSE101581_DNaseI_embryos_macs_peak_4	250	.	2.34192	26.656	25.0792	188
585	chr2L	21501	21858	GSE101581_DNaseI_embryos_macs_peak_5	898	.	3.83283	91.7741	89.8493	117
585	chr2L	26443	27303	GSE101581_DNaseI_embryos_macs_peak_6a	141	.	2.29571	15.6698	14.1961	125
585	chr2L	26443	27303	GSE101581_DNaseI_embryos_macs_peak_6b	32	.	1.61509	4.52759	3.21942	482

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.