Schema for PolII ChIP-Seq (Cell Lines) - RNA Polymerase II ChIP-Seq for Cell Lines

Database: dm6 Primary Table: EMBL_PolII_S2_macs Row Count: 40,156 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	5583	`int(10) unsigned`	range
`chromEnd`	5999	`int(10) unsigned`	range
`name`	PolII_S2_macs_peak_1	`varchar(255)`	values
`score`	287	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	2.90109	`float`	range
`pValue`	30.2774	`float`	range
`qValue`	28.7036	`float`	range
`peak`	267	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	5583	5999	PolII_S2_macs_peak_1	287	.	2.90109	30.2774	28.7036	267
585	chr2L	7738	8055	PolII_S2_macs_peak_2	76	.	1.9312	8.84079	7.65218	220
585	chr2L	8713	9422	PolII_S2_macs_peak_3a	170	.	2.22181	18.3936	17.0004	174
585	chr2L	8713	9422	PolII_S2_macs_peak_3b	161	.	2.30295	17.5385	16.1607	485
585	chr2L	11770	11967	PolII_S2_macs_peak_4	92	.	2.07531	10.5292	9.2973	108
585	chr2L	12070	12242	PolII_S2_macs_peak_5	40	.	1.66153	5.13384	4.06006	105
585	chr2L	12342	13032	PolII_S2_macs_peak_6a	147	.	2.22376	16.1279	14.776	137
585	chr2L	12342	13032	PolII_S2_macs_peak_6b	94	.	2.06312	10.6713	9.43621	487
585	chr2L	13496	14113	PolII_S2_macs_peak_7a	30	.	1.63889	4.11444	3.08013	80
585	chr2L	13496	14113	PolII_S2_macs_peak_7b	122	.	2.11972	13.5882	12.2872	458

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

PolII ChIP-Seq (Cell Lines) (cells_polII_chipseq) Track Description


	Description These tracks show the regions in the D. melanogaster genome that are significantly enriched in RNA Polymerase II (PolII) in different cell lines 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 Irreproducible Discovery Rate (IDR) peak calls were produced by the idr program using a global IDR threshold of 0.05. The RNA PolII ChIP-Seq reads for the S2 cells were obtained from the EBI ENA database under the accession number PRJEB3031. The antibody used in this study recognizes the Rpb3 subunit of RNA PolII. References Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137. doi: 10.1186/gb-2008-9-9-r137. Epub 2008 Sep 17.

Description