Schema for modENCODE PolII ChIP-Seq - modENCODE RNA Polymerase II ChIP-Seq

Database: dm6 Primary Table: Pupae_PolII_macs Row Count: 6,516 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	18209	`int(10) unsigned`	range
`chromEnd`	18694	`int(10) unsigned`	range
`name`	dm6_Pupae_PolII_peak_1	`varchar(255)`	values
`score`	707	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	13.6049	`float`	range
`pValue`	73.4639	`float`	range
`qValue`	70.74	`float`	range
`peak`	272	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	18209	18694	dm6_Pupae_PolII_peak_1	707	.	13.6049	73.4639	70.74	272
585	chr2L	21156	21492	dm6_Pupae_PolII_peak_2	388	.	8.19977	41.2233	38.8097	137
585	chr2L	58967	59444	dm6_Pupae_PolII_peak_3	913	.	16.7875	94.2343	91.3028	278
585	chr2L	66987	67236	dm6_Pupae_PolII_peak_4	105	.	3.39914	12.5672	10.5545	115
585	chr2L	72420	72859	dm6_Pupae_PolII_peak_5	658	.	8.24056	68.5467	65.8699	228
585	chr2L	87271	87535	dm6_Pupae_PolII_peak_6	138	.	4.59736	15.8809	13.8014	116
585	chr2L	106362	106731	dm6_Pupae_PolII_peak_7	56	.	2.65489	7.50651	5.62847	232
585	chr2L	107889	108412	dm6_Pupae_PolII_peak_8	1355	.	17.2718	138.98	135.529	256
585	chr2L	120366	120905	dm6_Pupae_PolII_peak_9	105	.	4.90032	12.5227	10.511	213
585	chr2L	121497	121939	dm6_Pupae_PolII_peak_10	1138	.	13.7144	117.07	113.888	218

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

modENCODE PolII ChIP-Seq (modENCODE_polII_chipseq) Track Description


	Description These tracks show the regions in the genome that are significantly enriched in RNA Polymerase II ChIP-Seq reads at different developmental stages as determined by MACS2. The signal tracks correspond to the log likelihood enrichment ratios of the treatment versus the DNA input sample as determined by the bdgcmp program in MACS2. The ChIP-Seq data were produced as part of the modENCODE project and were obtained from the NCBI Sequence Reads Archive under the accession number SRP001424. Credits Ho JW et al. ChIP-chip versus ChIP-seq: lessons for experimental design and data analysis. BMC Genomics. 2011 Feb 28;12:134. Zhang Y et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137.

Description