GSE31363, Transcription Factor Binding Sites by Epitope-Tag ChIP-seq from ENCODE/University of Chicago

Description:

This samples serie was produced as part of the ENCODE Project on TFBS. These samples represent several Transcription Factor binding sites in K562 cell line. The mapping uses expressed transcription factors as GFP-tagged fusion proteins after bacterial artificial chromosome (BAC) recombineering (recombination-mediated genetic engineering). Additional peak files are also provided.

Source

Files downloaded from the UCSC Genome Browser via URL: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUchicagoTfbs
Input file format: BAM and narrowPeak

Samples

From Human Feb. 2009 (GRCh37/hg19) Assembly

Filename Description Feature GEO-ID
1 wgEncodeUchicagoTfbsK562EfosControlAlnRep1.sga K562 - eGFP-FOS - Rep1 eGFP-FOS GSM777644
2 wgEncodeUchicagoTfbsK562EfosControlfosAlnRep2.sga K562 - eGFP-FOS - Rep2 eGFP-FOS GSM777644
3 wgEncodeUchicagoTfbsK562EfosControlfosAlnRep3.sga K562 - eGFP-FOS - Rep3 eGFP-FOS GSM777644
4 wgEncodeUchicagoTfbsK562Egata2ControlAlnRep1.sga K562 - eGFP-GATA2 - Rep1 eGFP-GATA2 GSM777641
5 wgEncodeUchicagoTfbsK562Egata2Controlgata2AlnRep2.sga K562 - eGFP-GATA2 - Rep2 eGFP-GATA2 GSM777641
6 wgEncodeUchicagoTfbsK562Ehdac8ControlAlnRep1.sga K562 - eGFP-HDAC8 - Rep1 eGFP-HDAC8 GSM777640
7 wgEncodeUchicagoTfbsK562Ehdac8Controlhdac8AlnRep2.sga K562 - eGFP-HDAC8 - Rep2 eGFP-HDAC8 GSM777640
8 wgEncodeUchicagoTfbsK562EjunbControlAlnRep1.sga K562 - eGFP-JunB - Rep1 eGFP-JunB GSM777638
9 wgEncodeUchicagoTfbsK562EjunbControljunbAlnRep2.sga K562 - eGFP-JunB - Rep2 eGFP-JunB GSM777638
10 wgEncodeUchicagoTfbsK562EjundControlAlnRep1.sga K562 - eGFP-JunD - Rep1 eGFP-JunD GSM777639
11 wgEncodeUchicagoTfbsK562EjundControljundAlnRep2.sga K562 - eGFP-JunD - Rep2 eGFP-JunD GSM777639
12 wgEncodeUchicagoTfbsK562EjundControljundAlnRep3.sga K562 - eGFP-JunD - Rep3 eGFP-JunD GSM777639
13 wgEncodeUchicagoTfbsK562Enr4a1ControlAlnRep1.sga K562 - eGFP-NR4A1 - Rep1 eGFP-NR4A1 GSM777637
14 wgEncodeUchicagoTfbsK562Enr4a1Controlnr4a1AlnRep2.sga K562 - eGFP-NR4A1 - Rep2 eGFP-NR4A1 GSM777637
15 wgEncodeUchicagoTfbsK562InputControlfosAlnRep1.sga K562 - Input - Control_eGFP-FOS - Rep1 Input GSM777646
16 wgEncodeUchicagoTfbsK562InputControlfosAlnRep2.sga K562 - Input - Control_eGFP-FOS - Rep2 Input GSM777646
17 wgEncodeUchicagoTfbsK562InputControlfosAlnRep3.sga K562 - Input - Control_eGFP-FOS - Rep3 Input GSM777646
18 wgEncodeUchicagoTfbsK562InputControlgata2AlnRep1.sga K562 - Input - Control_eGFP-GATA2 - Rep1 Input GSM777648
19 wgEncodeUchicagoTfbsK562InputControlgata2AlnRep2.sga K562 - Input - Control_eGFP-GATA2 - Rep2 Input GSM777648
20 wgEncodeUchicagoTfbsK562InputControlhdac8AlnRep1.sga K562 - Input - Control_eGFP-HDAC8 - Rep1 Input GSM777647
21 wgEncodeUchicagoTfbsK562InputControlhdac8AlnRep2.sga K562 - Input - Control_eGFP-HDAC8 - Rep2 Input GSM777647
22 wgEncodeUchicagoTfbsK562InputControljunbAlnRep1.sga K562 - Input - Control_eGFP-JunB - Rep1 Input GSM777643
23 wgEncodeUchicagoTfbsK562InputControljunbAlnRep2.sga K562 - Input - Control_eGFP-JunB - Rep2 Input GSM777643
24 wgEncodeUchicagoTfbsK562InputControljundAlnRep1.sga K562 - Input - Control_eGFP-JunD - Rep1 Input GSM777642
25 wgEncodeUchicagoTfbsK562InputControljundAlnRep2.sga K562 - Input - Control_eGFP-JunD - Rep2 Input GSM777642
26 wgEncodeUchicagoTfbsK562InputControljundAlnRep3.sga K562 - Input - Control_eGFP-JunD - Rep3 Input GSM777642
27 wgEncodeUchicagoTfbsK562InputControlnr4a1AlnRep1.sga K562 - Input - Control_eGFP-NR4A1 - Rep1 Input GSM777645
28 wgEncodeUchicagoTfbsK562InputControlnr4a1AlnRep2.sga K562 - Input - Control_eGFP-NR4A1 - Rep2 Input GSM777645

Peak Files [Human Feb. 2009 (GRCh37/hg19) Assembly]

Filename Description Feature GEO-ID
1 wgEncodeUchicagoTfbsK562EfosControlPk_peak.sga K562 - eGFP-FOS - peaks eGFP-FOS_P GSM777644
2 wgEncodeUchicagoTfbsK562Egata2ControlPk_peak.sga K562 - eGFP-GATA2 - peaks eGFP-GATA2_P GSM777641
3 wgEncodeUchicagoTfbsK562Ehdac8ControlPk_peak.sga K562 - eGFP-HDAC8 - peaks eGFP-HDAC8_P GSM777640
4 wgEncodeUchicagoTfbsK562EjunbControlPk_peak.sga K562 - eGFP-JunB - peaks eGFP-JunB_P GSM777638
5 wgEncodeUchicagoTfbsK562EjundControlPk_peak.sga K562 - eGFP-JunD - peaks eGFP-JunD_P GSM777639
6 wgEncodeUchicagoTfbsK562Enr4a1ControlPk_peak.sga K562 - eGFP-NR4A1 - peaks eGFP-NR4A1_P GSM777637

Technical Notes

BAM and narrowPeak files were downloaded from UCSC and converted in sga format using bamToBed (SamTools) and bed2sga (ChIP-seq).

References

  1. GEO series GSE31363 Transcription Factor Binding Sites by Epitope-Tag ChIP-seq from ENCODE/University of Chicago