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_macs Row Count: 291 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	73154	`int(10) unsigned`	range
`chromEnd`	73396	`int(10) unsigned`	range
`name`	GSE19025_NHS_HSF_KD_macs_pe...	`varchar(255)`	values
`score`	368	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	10.7804	`float`	range
`pValue`	40.8296	`float`	range
`qValue`	36.8572	`float`	range
`peak`	121	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	73154	73396	GSE19025_NHS_HSF_KD_macs_peak_1	368	.	10.7804	40.8296	36.8572	121
588	chr2L	490144	490380	GSE19025_NHS_HSF_KD_macs_peak_2	1040	.	16.7399	108.879	104.014	111
588	chr2L	492353	492521	GSE19025_NHS_HSF_KD_macs_peak_3	101	.	4.76545	13.6837	10.1133	102
589	chr2L	602415	602587	GSE19025_NHS_HSF_KD_macs_peak_4	176	.	6.91241	21.3983	17.691	87
590	chr2L	740131	740332	GSE19025_NHS_HSF_KD_macs_peak_5	691	.	11.4316	73.5632	69.1893	96
593	chr2L	1108280	1108445	GSE19025_NHS_HSF_KD_macs_peak_6	255	.	6.30343	29.3573	25.5336	84
595	chr2L	1362340	1362539	GSE19025_NHS_HSF_KD_macs_peak_7	389	.	8.89638	42.938	38.9417	87
596	chr2L	1491942	1492075	GSE19025_NHS_HSF_KD_macs_peak_8	134	.	4.95824	17.0657	13.4289	66
608	chr2L	3094991	3095116	GSE19025_NHS_HSF_KD_macs_peak_9	77	.	4.08943	11.3145	7.79877	69
608	chr2L	3108364	3108583	GSE19025_NHS_HSF_KD_macs_peak_10	1029	.	18.4476	107.794	102.942	108

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.