Schema for MACS2 DHS - DNaseI Hypersensitive Sites Identified by MACS2

Database: dm6 Primary Table: uwstam_DNaseI_stage5_macs Row Count: 24,586 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	5538	`int(10) unsigned`	range
`chromEnd`	5982	`int(10) unsigned`	range
`name`	uwstam_DNaseI_stage5_macs_p...	`varchar(255)`	values
`score`	815	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	13.1903	`float`	range
`pValue`	83.9847	`float`	range
`qValue`	81.574	`float`	range
`peak`	250	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	5538	5982	uwstam_DNaseI_stage5_macs_peak_1a	815	.	13.1903	83.9847	81.574	250
585	chr2L	5538	5982	uwstam_DNaseI_stage5_macs_peak_1b	187	.	5.50391	20.6063	18.7206	362
585	chr2L	7590	7708	uwstam_DNaseI_stage5_macs_peak_2	31	.	2.47631	4.70799	3.16466	41
585	chr2L	7876	7965	uwstam_DNaseI_stage5_macs_peak_3	21	.	2.19665	3.63667	2.14882	37
585	chr2L	8754	9070	uwstam_DNaseI_stage5_macs_peak_4a	82	.	3.38622	9.98418	8.27855	89
585	chr2L	8754	9070	uwstam_DNaseI_stage5_macs_peak_4b	124	.	4.02916	14.2159	12.4278	186
585	chr2L	12475	12574	uwstam_DNaseI_stage5_macs_peak_5	43	.	2.68496	5.96616	4.37406	76
585	chr2L	15274	15382	uwstam_DNaseI_stage5_macs_peak_6	56	.	2.90923	7.24373	5.60681	34
585	chr2L	18268	18349	uwstam_DNaseI_stage5_macs_peak_7	117	.	3.47025	13.5722	11.7957	42
585	chr2L	18561	18695	uwstam_DNaseI_stage5_macs_peak_8	177	.	4.15259	19.6414	17.77	68

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.