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

Database: dm6 Primary Table: L3_PolII_macs Row Count: 5,100 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	18003	`int(10) unsigned`	range
`chromEnd`	18592	`int(10) unsigned`	range
`name`	dm6_L3_PolII_peak_1	`varchar(255)`	values
`score`	71	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	4.1132	`float`	range
`pValue`	9.37479	`float`	range
`qValue`	7.10076	`float`	range
`peak`	163	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	18003	18592	dm6_L3_PolII_peak_1	71	.	4.1132	9.37479	7.10076	163
585	chr2L	19454	19668	dm6_L3_PolII_peak_2	34	.	2.75561	5.35986	3.40903	117
585	chr2L	20822	21361	dm6_L3_PolII_peak_3a	38	.	2.95441	5.90503	3.8964	109
585	chr2L	20822	21361	dm6_L3_PolII_peak_3b	103	.	5.12566	12.804	10.3256	384
585	chr2L	67029	67260	dm6_L3_PolII_peak_4	109	.	3.96745	13.4206	10.9087	108
585	chr2L	72565	73091	dm6_L3_PolII_peak_5	153	.	3.68071	18.1135	15.3638	184
585	chr2L	108056	108633	dm6_L3_PolII_peak_6	207	.	4.47639	23.8057	20.798	206
585	chr2L	109055	109287	dm6_L3_PolII_peak_7	48	.	2.6524	6.95968	4.85697	105
585	chr2L	128634	129300	dm6_L3_PolII_peak_8	187	.	3.64249	21.6162	18.7036	519
586	chr2L	132057	132411	dm6_L3_PolII_peak_9	68	.	2.59537	9.14431	6.87992	105

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