Schema for hkCP dCP STARR-Seq - Housekeeping and Developmental Enhancers Identified by STARR-Seq

Database: dm6 Primary Table: X16_S2_STARRseq_macs Row Count: 5,659 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	18033	`int(10) unsigned`	range
`chromEnd`	19110	`int(10) unsigned`	range
`name`	X16_S2_STARRseq_macs_peak_1	`varchar(255)`	values
`score`	889	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	10.4416	`float`	range
`pValue`	91.4814	`float`	range
`qValue`	88.9357	`float`	range
`peak`	575	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	18033	19110	X16_S2_STARRseq_macs_peak_1	889	.	10.4416	91.4814	88.9357	575
585	chr2L	20988	22169	X16_S2_STARRseq_macs_peak_2	394	.	6.47838	41.5484	39.4165	479
585	chr2L	46999	47873	X16_S2_STARRseq_macs_peak_3	310	.	5.52799	33.1077	31.0709	475
585	chr2L	72716	74068	X16_S2_STARRseq_macs_peak_4	29	.	2.0422	4.40373	2.96517	445
585	chr2L	106700	108404	X16_S2_STARRseq_macs_peak_5	489	.	6.07189	51.1521	48.9271	1132
585	chr2L	109003	109908	X16_S2_STARRseq_macs_peak_6	130	.	3.20843	14.7903	13.0265	432
585	chr2L	120254	121456	X16_S2_STARRseq_macs_peak_7	4675	.	27.4865	471.855	467.585	579
585	chr2L	128475	129847	X16_S2_STARRseq_macs_peak_8a	28	.	1.92992	4.31954	2.88535	225
585	chr2L	128475	129847	X16_S2_STARRseq_macs_peak_8b	21	.	1.80471	3.5065	2.13486	800
586	chr2L	142984	143592	X16_S2_STARRseq_macs_peak_9	94	.	2.84999	11.0958	9.41046	348

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

hkCP dCP STARR-Seq (hkCpdCpStarrSeq) Track Description

Description

These tracks show the putative housekeeping (hkCP) and developmental (dCP) enhancers identified by STARR-Seq in S2 and OSC cells. The regions that are enriched in STARR-Seq reads were identified by MACS2. The log likelihood ratio evidence tracks were also produced by MACS2.

The STARR-Seq reporters used in this study are as follows:

Reporter	Description	Reporter Type
RpS12 (hkCP)	Ribosomal protein gene 12	Housekeeping
eEF1delta	Eukaryotic translation elongation factor 1 delta	Housekeeping
NipB	Cohesin loader Nipped-B	Housekeeping
X16	Putative splicing factor x16	Housekeeping
DSCP (dCP)	Derived from the even-skipped transcription factor	Developmental
pnr	Derived from the pannier transcription factor	Developmental

References

Zabidi MA, Arnold CD, Schernhuber K, Pagani M, Rath M, Frank O, Stark A. Enhancer-core-promoter specificity separates developmental and housekeeping gene regulation. Nature. 2015 Feb 26;518(7540):556-9.

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.