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

Database: dm6 Primary Table: pnr_S2_STARRseq_macs Row Count: 2,795 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	107352	`int(10) unsigned`	range
`chromEnd`	107968	`int(10) unsigned`	range
`name`	pnr_S2_STARRseq_macs_peak_1	`varchar(255)`	values
`score`	36	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	2.75465	`float`	range
`pValue`	5.52474	`float`	range
`qValue`	3.68435	`float`	range
`peak`	424	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	107352	107968	pnr_S2_STARRseq_macs_peak_1	36	.	2.75465	5.52474	3.68435	424
585	chr2L	109298	110256	pnr_S2_STARRseq_macs_peak_2	46	.	2.87126	6.57372	4.64438	461
585	chr2L	120146	121499	pnr_S2_STARRseq_macs_peak_3	14257	.	107.756	1432.5	1425.78	691
586	chr2L	136475	137236	pnr_S2_STARRseq_macs_peak_4	39	.	2.91369	5.79459	3.925	656
586	chr2L	155228	155873	pnr_S2_STARRseq_macs_peak_5	69	.	3.3661	9.00934	6.9402	289
586	chr2L	161401	162351	pnr_S2_STARRseq_macs_peak_6	337	.	7.99521	36.4251	33.748	513
586	chr2L	165268	167211	pnr_S2_STARRseq_macs_peak_7a	52	.	3.13271	7.19522	5.22547	290
586	chr2L	165268	167211	pnr_S2_STARRseq_macs_peak_7b	417	.	8.62176	44.5567	41.7767	1471
586	chr2L	224021	225686	pnr_S2_STARRseq_macs_peak_8a	127	.	4.25126	15.072	12.792	391
586	chr2L	224021	225686	pnr_S2_STARRseq_macs_peak_8b	42	.	2.91633	6.16815	4.27243	1503

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.