Schema for MACS2 DHS - DNaseI Hypersensitive Sites Identified by MACS2

Database: dm6 Primary Table: uwstam_DNaseI_stage11_macs Row Count: 25,413 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	5595	`int(10) unsigned`	range
`chromEnd`	5728	`int(10) unsigned`	range
`name`	uwstam_DNaseI_stage11_macs_...	`varchar(255)`	values
`score`	38	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	2.86609	`float`	range
`pValue`	5.4865	`float`	range
`qValue`	3.83776	`float`	range
`peak`	80	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	5595	5728	uwstam_DNaseI_stage11_macs_peak_1	38	.	2.86609	5.4865	3.83776	80
585	chr2L	5761	5951	uwstam_DNaseI_stage11_macs_peak_2	112	.	4.50386	13.1581	11.272	130
585	chr2L	8823	8929	uwstam_DNaseI_stage11_macs_peak_3	38	.	2.86609	5.4865	3.83776	84
585	chr2L	18593	18707	uwstam_DNaseI_stage11_macs_peak_4	274	.	6.15478	29.5628	27.4059	59
585	chr2L	18848	19032	uwstam_DNaseI_stage11_macs_peak_5	421	.	7.79844	44.4726	42.1474	65
585	chr2L	21412	21516	uwstam_DNaseI_stage11_macs_peak_6	238	.	5.88172	25.965	23.856	50
585	chr2L	21682	21860	uwstam_DNaseI_stage11_macs_peak_7	875	.	12.4688	90.2536	87.5613	56
585	chr2L	27071	27291	uwstam_DNaseI_stage11_macs_peak_8	34	.	2.67282	5.12836	3.49873	69
585	chr2L	28011	28238	uwstam_DNaseI_stage11_macs_peak_9a	76	.	3.64093	9.41318	7.62388	72
585	chr2L	28011	28238	uwstam_DNaseI_stage11_macs_peak_9b	52	.	3.125	6.96909	5.26076	187

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.