Schema for MACS2 DHS - DNaseI Hypersensitive Sites Identified by MACS2

Database: dm6 Primary Table: GSE40739_DNaseI_OSC_macs Row Count: 26,188 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	5560	`int(10) unsigned`	range
`chromEnd`	5967	`int(10) unsigned`	range
`name`	GSE40739_DNaseI_OSC_macs_pe...	`varchar(255)`	values
`score`	3036	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	16.802	`float`	range
`pValue`	306.048	`float`	range
`qValue`	303.638	`float`	range
`peak`	145	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	5560	5967	GSE40739_DNaseI_OSC_macs_peak_1	3036	.	16.802	306.048	303.638	145
585	chr2L	6732	6873	GSE40739_DNaseI_OSC_macs_peak_2	29	.	2.07161	4.33839	2.9895	79
585	chr2L	18326	18447	GSE40739_DNaseI_OSC_macs_peak_3	53	.	2.46004	6.72383	5.31051	52
585	chr2L	18503	19004	GSE40739_DNaseI_OSC_macs_peak_4a	942	.	8.52143	96.2035	94.2425	138
585	chr2L	18503	19004	GSE40739_DNaseI_OSC_macs_peak_4b	1712	.	12.5867	173.364	171.202	325
585	chr2L	21520	21851	GSE40739_DNaseI_OSC_macs_peak_5a	234	.	4.53165	25.0699	23.4413	60
585	chr2L	21520	21851	GSE40739_DNaseI_OSC_macs_peak_5b	733	.	8.41593	75.2634	73.3753	242
585	chr2L	21899	22185	GSE40739_DNaseI_OSC_macs_peak_6a	240	.	4.53454	25.7264	24.0931	74
585	chr2L	21899	22185	GSE40739_DNaseI_OSC_macs_peak_6b	178	.	3.21745	19.4792	17.8983	225
585	chr2L	42197	42361	GSE40739_DNaseI_OSC_macs_peak_7	530	.	5.3273	54.8842	53.0807	77

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.