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

Database: dm6 Primary Table: E8_12_PolII_macs Row Count: 79 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	652	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	8809940	`int(10) unsigned`	range
`chromEnd`	8810017	`int(10) unsigned`	range
`name`	dm6_E8-12_PolII_peak_1	`varchar(255)`	values
`score`	21	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	3.79676	`float`	range
`pValue`	6.17367	`float`	range
`qValue`	2.17608	`float`	range
`peak`	39	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
652	chr2L	8809940	8810017	dm6_E8-12_PolII_peak_1	21	.	3.79676	6.17367	2.17608	39
726	chr2L	18592811	18592867	dm6_E8-12_PolII_peak_2	27	.	4.92455	6.85846	2.74191	7
748	chr2L	21440573	21440627	dm6_E8-12_PolII_peak_3	58	.	3.96597	10.2891	5.88605	23
647	chr2R	8232435	8232510	dm6_E8-12_PolII_peak_4	54	.	5.91093	9.84673	5.47812	50
661	chr2R	10078249	10078310	dm6_E8-12_PolII_peak_5	49	.	5.8793	9.29101	4.95172	32
676	chr2R	11989198	11989273	dm6_E8-12_PolII_peak_6	25	.	4.53691	6.6833	2.58587	3
761	chr3L	23114881	23114937	dm6_E8-12_PolII_peak_7	38	.	2.67331	8.08262	3.83825	24
594	chr3R	1272025	1272162	dm6_E8-12_PolII_peak_8a	153	.	4.61531	20.5098	15.3013	32
594	chr3R	1272025	1272162	dm6_E8-12_PolII_peak_8b	60	.	3.06171	10.4263	6.01316	101
622	chr3R	4852661	4852733	dm6_E8-12_PolII_peak_9	21	.	4.16414	6.11624	2.1341	12

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