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

Database: dm6 Primary Table: NipB_S2_STARRseq_macs Row Count: 7,188 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	13958	`int(10) unsigned`	range
`chromEnd`	14872	`int(10) unsigned`	range
`name`	NipB_S2_STARRseq_macs_peak_1	`varchar(255)`	values
`score`	44	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	2.25924	`float`	range
`pValue`	5.91398	`float`	range
`qValue`	4.48414	`float`	range
`peak`	367	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	13958	14872	NipB_S2_STARRseq_macs_peak_1	44	.	2.25924	5.91398	4.48414	367
585	chr2L	18383	19001	NipB_S2_STARRseq_macs_peak_2	84	.	3.08469	10.0401	8.44454	313
585	chr2L	35507	36145	NipB_S2_STARRseq_macs_peak_3	46	.	2.30024	6.10919	4.67174	318
585	chr2L	47030	48021	NipB_S2_STARRseq_macs_peak_4	666	.	8.72743	69.4266	66.6534	496
585	chr2L	66747	67438	NipB_S2_STARRseq_macs_peak_5	66	.	2.73762	8.12875	6.60227	307
585	chr2L	72245	74134	NipB_S2_STARRseq_macs_peak_6a	41	.	2.23173	5.55639	4.1452	584
585	chr2L	72245	74134	NipB_S2_STARRseq_macs_peak_6b	42	.	2.36437	5.649	4.23401	1714
585	chr2L	104666	105351	NipB_S2_STARRseq_macs_peak_7	69	.	2.5353	8.51187	6.97024	377
585	chr2L	106535	110094	NipB_S2_STARRseq_macs_peak_8a	61	.	2.53905	7.66265	6.15482	246
585	chr2L	106535	110094	NipB_S2_STARRseq_macs_peak_8b	679	.	7.51074	70.7218	67.9291	1344

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.