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

Database: dm6 Primary Table: E20_24_PolII_macs Row Count: 208 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	108120	`int(10) unsigned`	range
`chromEnd`	108275	`int(10) unsigned`	range
`name`	dm6_E20-24_PolII_peak_1	`varchar(255)`	values
`score`	50	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	6.07919	`float`	range
`pValue`	8.91689	`float`	range
`qValue`	5.04374	`float`	range
`peak`	88	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	108120	108275	dm6_E20-24_PolII_peak_1	50	.	6.07919	8.91689	5.04374	88
585	chr2L	129125	129287	dm6_E20-24_PolII_peak_2	50	.	6.33317	8.91689	5.04374	78
587	chr2L	285624	285758	dm6_E20-24_PolII_peak_3	50	.	6.07919	8.91689	5.04374	65
590	chr2L	740126	740314	dm6_E20-24_PolII_peak_4	224	.	13.4448	28.0718	22.4826	95
591	chr2L	850938	851203	dm6_E20-24_PolII_peak_5	83	.	5.80498	12.6839	8.37068	161
593	chr2L	1077744	1077934	dm6_E20-24_PolII_peak_6	28	.	4.58159	6.33154	2.85723	92
593	chr2L	1118883	1119053	dm6_E20-24_PolII_peak_7	40	.	5.28561	7.69019	4.02982	81
595	chr2L	1420338	1420513	dm6_E20-24_PolII_peak_8	92	.	7.17532	13.6958	9.29055	78
597	chr2L	1651208	1651397	dm6_E20-24_PolII_peak_9	95	.	7.39423	13.9554	9.54527	90
599	chr2L	1884612	1884755	dm6_E20-24_PolII_peak_10	61	.	5.82583	10.2186	6.19432	69

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