Schema for Heat Shock Proteins ChIP-Seq (S2) - ChIP-Seq of Heat Shock Proteins in S2 Cells

Database: dm6 Primary Table: GSE19025_NHS_HSF_KD_peakzilla Row Count: 5,175 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	69451	`int(10) unsigned`	range
`chromEnd`	69689	`int(10) unsigned`	range
`name`	peakzilla_7216	`varchar(255)`	values
`score`	1	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	3.71	`float`	range
`pValue`	-1	`float`	range
`qValue`	0.28291	`float`	range
`peak`	119	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	69451	69689	peakzilla_7216	1	.	3.71	-1	0.28291	119
585	chr2L	73166	73404	peakzilla_142	12	.	36.73	-1	309.653	119
585	chr2L	76468	76706	peakzilla_3850	2	.	2.62	-1	0.27761	119
585	chr2L	128436	128674	peakzilla_1854	2	.	6.63	-1	0.2926	119
586	chr2L	185402	185640	peakzilla_1415	2	.	4.24	-1	0.30856	119
586	chr2L	245985	246223	peakzilla_8158	1	.	2.66	-1	0.28492	119
587	chr2L	266218	266456	peakzilla_6361	1	.	2.18	-1	0.27835	119
587	chr2L	295039	295277	peakzilla_561	3	.	6.68	-1	0.55893	119
587	chr2L	322536	322774	peakzilla_3485	2	.	2.85	-1	0.27811	119
588	chr2L	405198	405436	peakzilla_2353	2	.	3.67	-1	0.28391	119

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

Heat Shock Proteins ChIP-Seq (S2) (hspChIPSeq) Track Description

Description

These tracks show the results of the ChIP-Seq analyses of heat shock proteins from S2 cells. The regions that are enriched in the heat shock proteins were identified by MACS2 and Peakzilla. The log likelihood ratio evidence tracks were produced by MACS2. The Irreproducible Discovery Rate (IDR) peak calls were produced by the idr program using a global IDR threshold of 0.05.

The ChIP-Seq datasets were obtained from the Gene Expression Omnibus database at NCBI under the following accession numbers:

Accession	Proteins	Reference
GSE31226	Hsp90	Sawarkar R et al., Cell. 2012
GSE19025	HSF, HSF RNAi Knockdown	Guertin MJ et al., PLoS Genet. 2010

References

Sawarkar R, Sievers C, Paro R. Hsp90 globally targets paused RNA polymerase to regulate gene expression in response to environmental stimuli. Cell. 2012 May 11;149(4):807-18.

Guertin MJ, Lis JT. Chromatin landscape dictates HSF binding to target DNA elements. PLoS Genet. 2010 Sep 9;6(9):e1001114.

Bardet AF, Steinmann J, Bafna S, Knoblich JA, Zeitlinger J, Stark A. Identification of transcription factor binding sites from ChIP-seq data at high resolution. Bioinformatics. 2013 Nov 1;29(21):2705-13.

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.