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

Database: dm6 Primary Table: E16_20_PolII_macs Row Count: 14,729 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	7822	`int(10) unsigned`	range
`chromEnd`	7994	`int(10) unsigned`	range
`name`	dm6_E16-20_PolII_peak_1	`varchar(255)`	values
`score`	34	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	3.54605	`float`	range
`pValue`	5.12718	`float`	range
`qValue`	3.40634	`float`	range
`peak`	135	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	7822	7994	dm6_E16-20_PolII_peak_1	34	.	3.54605	5.12718	3.40634	135
585	chr2L	8808	9030	dm6_E16-20_PolII_peak_2	60	.	4.63999	8.12735	6.04663	95
585	chr2L	36888	37067	dm6_E16-20_PolII_peak_3	22	.	2.9744	3.84744	2.28511	65
585	chr2L	39517	39709	dm6_E16-20_PolII_peak_4	42	.	3.70057	6.04467	4.23263	178
585	chr2L	43408	43618	dm6_E16-20_PolII_peak_5	41	.	3.51203	5.94583	4.1355	79
585	chr2L	68093	68238	dm6_E16-20_PolII_peak_6	31	.	2.71253	4.83877	3.1635	101
585	chr2L	73578	73796	dm6_E16-20_PolII_peak_7	52	.	3.97582	7.22233	5.26029	118
585	chr2L	83867	84077	dm6_E16-20_PolII_peak_8	53	.	4.4212	7.3371	5.33187	138
585	chr2L	86480	86679	dm6_E16-20_PolII_peak_9	70	.	4.80404	9.25272	7.08057	95
585	chr2L	91582	91842	dm6_E16-20_PolII_peak_10	85	.	5.42505	10.9285	8.55955	128

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