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

Database: dm6 Primary Table: GSE19025_20HS_HSF_KD_macs Row Count: 256 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	73131	`int(10) unsigned`	range
`chromEnd`	73395	`int(10) unsigned`	range
`name`	GSE19025_20HS_HSF_KD_macs_p...	`varchar(255)`	values
`score`	261	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	8.76959	`float`	range
`pValue`	29.9865	`float`	range
`qValue`	26.1191	`float`	range
`peak`	149	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	73131	73395	GSE19025_20HS_HSF_KD_macs_peak_1	261	.	8.76959	29.9865	26.1191	149
587	chr2L	295061	295205	GSE19025_20HS_HSF_KD_macs_peak_2	154	.	6.62565	19.1746	15.4634	67
588	chr2L	490137	490377	GSE19025_20HS_HSF_KD_macs_peak_3	818	.	14.2907	86.3053	81.8333	114
590	chr2L	740132	740334	GSE19025_20HS_HSF_KD_macs_peak_4	521	.	9.61296	56.3638	52.1996	100
596	chr2L	1491921	1492055	GSE19025_20HS_HSF_KD_macs_peak_5	118	.	4.64574	15.535	11.8938	70
608	chr2L	3108359	3108575	GSE19025_20HS_HSF_KD_macs_peak_6	748	.	14.9526	79.2528	74.8604	103
611	chr2L	3472354	3472530	GSE19025_20HS_HSF_KD_macs_peak_7	466	.	10.0723	50.7181	46.6144	91
612	chr2L	3657371	3657577	GSE19025_20HS_HSF_KD_macs_peak_8	459	.	12.3875	50.0751	45.9758	103
613	chr2L	3786286	3786534	GSE19025_20HS_HSF_KD_macs_peak_9	617	.	14.7994	66.0109	61.7505	129
614	chr2L	3813370	3813569	GSE19025_20HS_HSF_KD_macs_peak_10	455	.	10.9784	49.6045	45.5134	97

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.