Schema for MACS2 DHS - DNaseI Hypersensitive Sites Identified by MACS2

Database: dm6 Primary Table: GSE101581_DNaseI_Mef2_macs Row Count: 23,202 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	5569	`int(10) unsigned`	range
`chromEnd`	6061	`int(10) unsigned`	range
`name`	GSE101581_DNaseI_Mef2_macs_...	`varchar(255)`	values
`score`	1992	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	8.68895	`float`	range
`pValue`	201.356	`float`	range
`qValue`	199.24	`float`	range
`peak`	313	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	5569	6061	GSE101581_DNaseI_Mef2_macs_peak_1	1992	.	8.68895	201.356	199.24	313
585	chr2L	6901	7073	GSE101581_DNaseI_Mef2_macs_peak_2	71	.	2.01269	8.51962	7.13646	91
585	chr2L	7365	7809	GSE101581_DNaseI_Mef2_macs_peak_3	377	.	3.65721	39.4196	37.7974	214
585	chr2L	8190	8516	GSE101581_DNaseI_Mef2_macs_peak_4a	73	.	2.02105	8.7762	7.39086	130
585	chr2L	8190	8516	GSE101581_DNaseI_Mef2_macs_peak_4b	49	.	1.82189	6.29609	4.94992	260
585	chr2L	8644	9062	GSE101581_DNaseI_Mef2_macs_peak_5a	20	.	1.53055	3.36006	2.08186	89
585	chr2L	8644	9062	GSE101581_DNaseI_Mef2_macs_peak_5b	130	.	2.37708	14.4829	13.0315	258
585	chr2L	18179	19194	GSE101581_DNaseI_Mef2_macs_peak_6a	1732	.	5.07224	175.273	173.212	153
585	chr2L	18179	19194	GSE101581_DNaseI_Mef2_macs_peak_6b	15799	.	19.0346	1583.68	1579.97	449
585	chr2L	20481	20695	GSE101581_DNaseI_Mef2_macs_peak_7	120	.	1.85634	13.4577	12.0171	151

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.