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

Database: dm6 Primary Table: E12_16_PolII_macs Row Count: 4,776 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	7616	`int(10) unsigned`	range
`chromEnd`	7957	`int(10) unsigned`	range
`name`	dm6_E12-16_PolII_peak_1	`varchar(255)`	values
`score`	50	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	3.02126	`float`	range
`pValue`	7.05104	`float`	range
`qValue`	5.04644	`float`	range
`peak`	186	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	7616	7957	dm6_E12-16_PolII_peak_1	50	.	3.02126	7.05104	5.04644	186
585	chr2L	18133	18605	dm6_E12-16_PolII_peak_2	223	.	5.31095	24.8002	22.3935	304
585	chr2L	20712	21410	dm6_E12-16_PolII_peak_3	230	.	6.20075	25.4634	23.0466	532
585	chr2L	59018	59420	dm6_E12-16_PolII_peak_4	139	.	3.69396	16.1655	13.9093	215
585	chr2L	66949	67289	dm6_E12-16_PolII_peak_5	193	.	4.57187	21.7486	19.3911	173
585	chr2L	72535	72876	dm6_E12-16_PolII_peak_6	50	.	2.59047	7.0109	5.0079	147
585	chr2L	87140	87529	dm6_E12-16_PolII_peak_7	346	.	7.78133	37.2251	34.6514	207
585	chr2L	102397	102640	dm6_E12-16_PolII_peak_8	32	.	2.51794	5.1199	3.2251	207
585	chr2L	106474	106724	dm6_E12-16_PolII_peak_9	151	.	4.63653	17.4772	15.1951	119
585	chr2L	107954	108429	dm6_E12-16_PolII_peak_10	1163	.	13.179	119.821	116.344	222

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