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

Database: dm6 Primary Table: GSE19025_NHS_HSF_macs Row Count: 242 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	73156	`int(10) unsigned`	range
`chromEnd`	73375	`int(10) unsigned`	range
`name`	GSE19025_NHS_HSF_macs_peak_1	`varchar(255)`	values
`score`	178	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	7.54777	`float`	range
`pValue`	21.7796	`float`	range
`qValue`	17.8221	`float`	range
`peak`	101	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	73156	73375	GSE19025_NHS_HSF_macs_peak_1	178	.	7.54777	21.7796	17.8221	101
587	chr2L	295061	295217	GSE19025_NHS_HSF_macs_peak_2	267	.	9.56844	30.9001	26.7789	69
588	chr2L	490156	490350	GSE19025_NHS_HSF_macs_peak_3	888	.	15.6939	93.9224	88.8649	96
588	chr2L	492373	492482	GSE19025_NHS_HSF_macs_peak_4	77	.	4.54858	11.5137	7.79117	54
590	chr2L	740152	740309	GSE19025_NHS_HSF_macs_peak_5	439	.	9.50771	48.3103	43.9251	76
593	chr2L	1108306	1108412	GSE19025_NHS_HSF_macs_peak_6	105	.	4.4705	14.316	10.5143	52
595	chr2L	1362353	1362494	GSE19025_NHS_HSF_macs_peak_7	319	.	8.64503	36.1128	31.9162	69
608	chr2L	3108381	3108553	GSE19025_NHS_HSF_macs_peak_8	643	.	14.8906	69.1124	64.3872	88
611	chr2L	3472369	3472516	GSE19025_NHS_HSF_macs_peak_9	206	.	7.0361	24.63	20.615	77
612	chr2L	3657411	3657572	GSE19025_NHS_HSF_macs_peak_10	155	.	7.27965	19.503	15.5843	76

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.