Schema for MACS2 DHS - DNaseI Hypersensitive Sites Identified by MACS2

Database: dm6 Primary Table: uwstam_DNaseI_stage9_macs Row Count: 13,873 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	5591	`int(10) unsigned`	range
`chromEnd`	5671	`int(10) unsigned`	range
`name`	uwstam_DNaseI_stage9_macs_p...	`varchar(255)`	values
`score`	38	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	4.20875	`float`	range
`pValue`	5.71384	`float`	range
`qValue`	3.83064	`float`	range
`peak`	56	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	5591	5671	uwstam_DNaseI_stage9_macs_peak_1	38	.	4.20875	5.71384	3.83064	56
585	chr2L	5757	5926	uwstam_DNaseI_stage9_macs_peak_2	148	.	8.72093	17.1705	14.8005	100
585	chr2L	18598	18694	uwstam_DNaseI_stage9_macs_peak_3	57	.	4.29293	7.74745	5.75111	39
585	chr2L	18905	19004	uwstam_DNaseI_stage9_macs_peak_4	64	.	4.53629	8.51793	6.48221	49
585	chr2L	21422	21502	uwstam_DNaseI_stage9_macs_peak_5	80	.	5.06073	10.2006	8.08825	44
585	chr2L	21689	21854	uwstam_DNaseI_stage9_macs_peak_6	149	.	6.97211	17.3224	14.948	63
585	chr2L	27053	27390	uwstam_DNaseI_stage9_macs_peak_7	115	.	5.89623	13.7767	11.5244	152
585	chr2L	27950	28321	uwstam_DNaseI_stage9_macs_peak_8a	91	.	5.27831	11.3454	9.18544	64
585	chr2L	27950	28321	uwstam_DNaseI_stage9_macs_peak_8b	135	.	6.47793	15.8397	13.5141	201
585	chr2L	28729	28809	uwstam_DNaseI_stage9_macs_peak_9	52	.	4.03226	7.23894	5.26591	46

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.