Schema for MACS2 DHS - DNaseI Hypersensitive Sites Identified by MACS2

Database: dm6 Primary Table: uwstam_DNaseI_Kc167_macs Row Count: 30,166 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	59265	`int(10) unsigned`	range
`chromEnd`	59367	`int(10) unsigned`	range
`name`	uwstam_DNaseI_Kc167_macs_pe...	`varchar(255)`	values
`score`	45	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	2.41328	`float`	range
`pValue`	5.98058	`float`	range
`qValue`	4.54398	`float`	range
`peak`	57	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	59265	59367	uwstam_DNaseI_Kc167_macs_peak_1	45	.	2.41328	5.98058	4.54398	57
585	chr2L	65083	65188	uwstam_DNaseI_Kc167_macs_peak_2	78	.	2.61003	9.37977	7.86331	49
585	chr2L	66258	66438	uwstam_DNaseI_Kc167_macs_peak_3	227	.	3.97614	24.523	22.7717	111
585	chr2L	66551	67532	uwstam_DNaseI_Kc167_macs_peak_4a	406	.	5.19731	42.6332	40.6839	148
585	chr2L	66551	67532	uwstam_DNaseI_Kc167_macs_peak_4b	1261	.	9.5941	128.684	126.118	412
585	chr2L	66551	67532	uwstam_DNaseI_Kc167_macs_peak_4c	430	.	5.17319	44.9994	43.0271	601
585	chr2L	66551	67532	uwstam_DNaseI_Kc167_macs_peak_4d	225	.	3.66209	24.2588	22.5104	855
585	chr2L	72260	73921	uwstam_DNaseI_Kc167_macs_peak_5a	80	.	2.04732	9.57956	8.05977	72
585	chr2L	72260	73921	uwstam_DNaseI_Kc167_macs_peak_5b	1139	.	6.17688	116.487	113.993	310
585	chr2L	72260	73921	uwstam_DNaseI_Kc167_macs_peak_5c	1839	.	8.10049	186.84	183.974	702

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.