# ################################## # TKA primers mapped to hg19 track TKA_Primers bigDataUrl Primers/TKA_primers_hg19.bb shortLabel TKA_primers longLabel Primers in the Archer Lab type bigBed exonArrows on colorByStrand 255,0,0 0,0,255 priority 1201 graphTypeDefault bar gridDefault on viewLimits 0:50 visibility full #################################### ## track set ## NextSeq data for ATAC Experiment track ATAC-NexSeq compositeTrack on shortLabel ATAC_NexSeq longLabel ATAC_NexSeq_NS50005_NS50031 type bigWig allButtonPair on centerLabelsDense on dragAndDrop on priority 1200 alwaysZero on graphTypeDefault bar maxHeightPixels 100:44:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on autoScale on viewLimits 0:50 visibility full # ################################## # bigWig coverage track # ATAC insertions siH1e track siH1e_InsertionSite parent ATAC-NexSeq bigDataUrl UL3_siH1e_NS50005_NS50031_Isite.bigwig shortLabel siH1e_insertion_sites longLabel siH1e ATAC UL3 insertion sites type bigWig color 0,255,64 priority 1201 alwaysZero on graphTypeDefault bar maxHeightPixels 100:44:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on autoScale on viewLimits 0:50 visibility full # ################################## # bigWig coverage track # ATAC siH1e track NC1_InsertionSite parent ATAC-NexSeq bigDataUrl UL3_NC1_NS50005_NS50031_Isite.bigwig shortLabel NC1_insertion_sites longLabel NC1 ATAC UL3 insertion sites type bigWig color 64,0,255 priority 1201 alwaysZero on graphTypeDefault bar maxHeightPixels 100:44:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on autoScale on viewLimits 0:50 visibility full # ################################## # bigWig coverage track # ATAC NFR coverage siH1e track siH1e_NFR parent ATAC-NexSeq bigDataUrl UL3_siH1e_NS50005_NS50031_NFR150.bigwig shortLabel siH1e_NFR150 longLabel siH1e ATAC UL3 150bp NFR reads type bigWig color 0,255,64 priority 1201 alwaysZero on graphTypeDefault bar maxHeightPixels 100:44:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on autoScale on viewLimits 0:50 visibility full # ################################## # bigWig coverage track # ATAC NFR coverage NC1 track NC1_NFR parent ATAC-NexSeq bigDataUrl UL3_NC1_NS50005_NS50031_NFR150.bigwig shortLabel NC1_NFR150 longLabel NC1 ATAC UL3 150bp NFR reads type bigWig color 64,0,255 priority 1201 alwaysZero on graphTypeDefault bar maxHeightPixels 100:44:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on autoScale on viewLimits 0:50 visibility full #################################### ## track set ## Peaks and Hotspots from ATAC-seq track ATAC_Peaks compositeTrack on shortLabel ATAC Peaks longLabel ATAC Peaks NS50005 NS50031 type bigBed allButtonPair on centerLabelsDense on dragAndDrop on priority 1200 graphTypeDefault bar maxHeightPixels 100:44:8 gridDefault on viewLimits 0:50 visibility full # ################################## # bigWig coverage track # ATAC insertions siH1e track siH1.4_Isite_Peaks parent ATAC_Peaks bigDataUrl ATAC_peaks/UL3_siH1e_NS50005_NS50031.fdr0.01.pks.bigbed shortLabel siH1e ISite peaks longLabel siH1e ATAC UL3 insertion site peaks type bigBed color 0,255,64 priority 1201 graphTypeDefault bar windowingFunction mean+whiskers gridDefault on viewLimits 0:50 visibility full # ################################## # bigWig coverage track # ATAC siH1e track siNC1_Isite_Peaks parent ATAC_Peaks bigDataUrl ATAC_peaks/UL3_NC1_NS50005_NS50031.fdr0.01.pks.bigbed shortLabel siNC1 Isite Peaks longLabel siNC1 ATAC UL3 insertion sites peaks type bigBed color 64,0,255 priority 1201 alwaysZero on maxHeightPixels 100:44:8 gridDefault on viewLimits 0:50 visibility full # ################################## # bigWig coverage track # ATAC NFR coverage siH1e track siH1.4_Peaks parent ATAC_Peaks bigDataUrl ATAC_peaks/UL3_siH1e_NS50005_NS50031_NFR150.fdr0.01.pks.bigbed shortLabel siH1.4 NFR150 peaks longLabel siH1.4 ATAC UL3 150bp NFR peaks type bigBed color 0,255,64 priority 1201 alwaysZero on maxHeightPixels 100:44:8 gridDefault on viewLimits 0:50 visibility full # ################################## # bigWig coverage track # ATAC NFR coverage NC1 track siNC1_Peaks parent ATAC_Peaks bigDataUrl ATAC_peaks/UL3_NC1_NS50005_NS50031_NFR150.fdr0.01.pks.bigbed shortLabel siNC1 peaks longLabel siNC1 ATAC UL3 150bp NFR peaks type bigBed color 64,0,255 priority 1201 alwaysZero on graphTypeDefault bar maxHeightPixels 100:44:8 gridDefault on autoScale on viewLimits 0:50 visibility full #################################### ## track set ## Hotspots and Hotspots from ATAC-seq track ATAC_Hotspots compositeTrack on shortLabel ATAC Hotspots longLabel ATAC Hotspots NS50005 NS50031 type bigBed allButtonPair on centerLabelsDense on dragAndDrop on priority 1200 graphTypeDefault bar maxHeightPixels 100:44:8 gridDefault on viewLimits 0:50 visibility full # ################################## # bigWig coverage track # ATAC insertions siH1e track siH1.4_Isite_Hotspots parent ATAC_Hotspots bigDataUrl ATAC_peaks/UL3_siH1e_NS50005_NS50031.fdr0.01.hot_cut.bigbed shortLabel siH1e ISite Hotspots longLabel siH1e ATAC UL3 insertion site Hotspots type bigBed color 0,255,64 priority 1201 graphTypeDefault bar windowingFunction mean+whiskers gridDefault on viewLimits 0:50 visibility full # ################################## # bigWig coverage track # ATAC siH1e track siNC1_Isite_Hotspots parent ATAC_Hotspots bigDataUrl ATAC_peaks/UL3_NC1_NS50005_NS50031.fdr0.01.hot_cut.bigbed shortLabel siNC1 Isite Hotspots longLabel siNC1 ATAC UL3 insertion sites Hotspots type bigBed color 64,0,255 priority 1201 alwaysZero on maxHeightPixels 100:44:8 gridDefault on viewLimits 0:50 visibility full # ################################## # bigWig coverage track # ATAC NFR coverage siH1e track siH1.4_Hotspots parent ATAC_Hotspots bigDataUrl ATAC_peaks/UL3_siH1e_NS50005_NS50031_NFR150.fdr0.01.hot_cut.bigbed shortLabel siH1.4 NFR150 Hotspots longLabel siH1.4 ATAC UL3 150bp NFR Hotspots type bigBed color 0,255,64 priority 1201 alwaysZero on maxHeightPixels 100:44:8 gridDefault on viewLimits 0:50 visibility full # ################################## # bigWig coverage track # ATAC NFR coverage NC1 track siNC1_Hotspots parent ATAC_Hotspots bigDataUrl ATAC_peaks/UL3_NC1_NS50005_NS50031_NFR150.fdr0.01.hot_cut.bigbed shortLabel siNC1 Hotspots longLabel siNC1 ATAC UL3 150bp NFR Hotspots type bigBed color 64,0,255 priority 1201 alwaysZero on graphTypeDefault bar maxHeightPixels 100:44:8 gridDefault on autoScale on viewLimits 0:50 visibility full #################################### ## track set ## Kim's scRNA track scRNA compositeTrack on shortLabel scRNA longLabel scRNA A1-2 +/- Dex type bigWig allButtonPair on centerLabelsDense on dragAndDrop on priority 1200 alwaysZero on graphTypeDefault bar maxHeightPixels 100:44:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on autoScale on viewLimits 0:50 visibility full # ################################## # bigWig coverage track # Veh scRNA track Veh parent scRNA bigDataUrl control.sorted.bw shortLabel Veh longLabel Veh scRNA A1-2 type bigWig color 111,151,22 priority 1201 alwaysZero on graphTypeDefault bar maxHeightPixels 100:44:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on autoScale on viewLimits 0:50 visibility full # ################################## # bigWig coverage track # Dex scRNA track Dex parent scRNA bigDataUrl dex.sorted.bw shortLabel Dex longLabel Dex scRNA A1-2 type bigWig color 0,0,128 priority 1201 alwaysZero on graphTypeDefault bar maxHeightPixels 100:44:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on autoScale on viewLimits 0:50 visibility full #################################### ## track set ## GR Binding Site data track GR_Binding_Sites compositeTrack on shortLabel GR_Peaks longLabel GR_ChIP-seq_peaks type bigBed allButtonPair on centerLabelsDense on dragAndDrop on priority 1200 alwaysZero on graphTypeDefault bar maxHeightPixels 100:44:8 smoothingWindow 2 transformFunc NONE gridDefault on autoScale on viewLimits 0:50 visibility full # ################################## # bigbed coverage track # A1-2 1hr GR binding sites track 1hr_GRBS parent GR_Binding_Sites bigDataUrl T47D_GR_1hr_hg19_Dex.bigBed shortLabel 1hr_GRBS_A1-2 longLabel 1hr GR ChIP-seq peaks A1-2 type bigBed color 0,0,128 priority 1201 alwaysZero on graphTypeDefault bar maxHeightPixels 100:44:8 smoothingWindow 2 transformFunc NONE gridDefault on autoScale on viewLimits 0:50 visibility full # ################################## # bigWig coverage track # A1-2 18hr GR binding sites track 18hr_GRBS parent GR_Binding_Sites bigDataUrl GR_18hr_A1-2.bigBed shortLabel 18hr_GRBS longLabel 18hr GR ChIP-seq peaks A1-2 type bigBed color 111,151,22 priority 1202 alwaysZero on graphTypeDefault bar maxHeightPixels 100:44:8 smoothingWindow 2 transformFunc NONE gridDefault on autoScale on viewLimits 0:50 visibility full # ################################## # bigWig coverage track # 1hr A549 GR peaks track A549_GRBS parent GR_Binding_Sites bigDataUrl A549_GR_1hr_Dex_peaks.bigbed shortLabel A549_1hr_GRBS longLabel 1hr GR ChIP-seq peaks A549 type bigBed color 128,64,64 priority 1203 alwaysZero on graphTypeDefault bar maxHeightPixels 100:44:8 smoothingWindow 2 transformFunc NONE gridDefault on autoScale on viewLimits 0:50 visibility full # ################################## # bigWig coverage track # 1hr UL3/U2O-S siNC1 GR peaks track UL3_NC1_GRBS parent GR_Binding_Sites bigDataUrl NC1_Dex_summits_200bp.bigbed shortLabel UL3_siNC1_GRBS longLabel 1hr GR ChIP-seq peaks UL3 siNC1 type bigBed color 128,0,255 priority 1204 alwaysZero on graphTypeDefault bar maxHeightPixels 100:44:8 smoothingWindow 2 transformFunc NONE gridDefault on autoScale on viewLimits 0:50 visibility full # ################################## # bigWig coverage track # 1hr UL3/U2O-S siH1.4 GR peaks track UL3_siH1e_GRBS parent GR_Binding_Sites bigDataUrl siH1e_Dex_summits_200bp.bigbed shortLabel UL3_siH1e_GRBS longLabel 1hr GR ChIP-seq peaks UL3 siH1e type bigBed color 0,255,64 priority 1205 alwaysZero on graphTypeDefault bar maxHeightPixels 100:44:8 smoothingWindow 2 transformFunc NONE gridDefault on autoScale on viewLimits 0:50 visibility full #################################### ## track set ## TSS data from scRNA track TSSs compositeTrack on shortLabel TSS longLabel rTSS_hg19 type bigBed allButtonPair on centerLabelsDense on dragAndDrop on priority 1200 alwaysZero on graphTypeDefault bar maxHeightPixels 100:44:8 smoothingWindow 2 transformFunc NONE gridDefault on autoScale on viewLimits 0:50 visibility full # ################################## # bigBed coverage track # refSeq Annotated TSSs track aTSS parent TSSs bigDataUrl refSeq_aTSS_hg19_sort.bigbed shortLabel aTSS longLabel annotated RefSeq TSSs type bigBed color 0,0,128 priority 1201 alwaysZero on graphTypeDefault bar maxHeightPixels 100:44:8 smoothingWindow 2 transformFunc NONE gridDefault on autoScale on viewLimits 0:50 visibility full # ################################## # bigBed coverage track # oTSSs from Veh scRNA in A1-2 cells track Veh_oTSS parent TSSs bigDataUrl scRNA_veh_oTSS_sort.bigbed shortLabel Veh_oTSS longLabel Dex oTSS plus refSeq TSSs type bigBed color 128,0,0 priority 1201 alwaysZero on graphTypeDefault bar maxHeightPixels 100:44:8 smoothingWindow 2 transformFunc NONE gridDefault on autoScale on viewLimits 0:50 visibility full # ################################## # bigBed coverage track # oTSSs from Veh scRNA in A1-2 cells track Dex_oTSS parent TSSs bigDataUrl scRNA_dex_oTSS_sort.bigbed shortLabel Dex_oTSS longLabel Dex oTSS plus refSeq TSSs type bigBed color 0,128,0 priority 1202 alwaysZero on graphTypeDefault bar maxHeightPixels 100:44:8 smoothingWindow 2 transformFunc NONE gridDefault on autoScale on viewLimits 0:50 visibility full #################################### ## track set ## GR ChIP-seq +/- siH1.4 track GR_ChIP-seq compositeTrack on shortLabel GR_ChIP-seq longLabel GR ChIP-seq UL3 siH1e NS50038 and MES661 type bigWig allButtonPair on centerLabelsDense on dragAndDrop on priority 1300 alwaysZero on graphTypeDefault bar maxHeightPixels 100:44:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on autoScale on viewLimits 0:50 visibility full # ################################## # bigWig coverage track # siNC1 Veh Input track siNC1_Veh_Input parent GR_ChIP-seq bigDataUrl MES661_141114_M00421_ABFD6.NC1-VehInput.1.sanger.cutAdapt.sickle.bowtie2_N1_hg19.filter.dedupe.merge.dedupe2.bs10_1xGenCov.bigwig shortLabel siNC1_Veh_Input longLabel siNC1 Veh Input UL3 type bigWig color 68,0,200 priority 1201 alwaysZero on graphTypeDefault bar maxHeightPixels 100:44:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on autoScale on viewLimits 0:50 visibility full # ################################## # bigWig coverage track # siNC1 Veh GR IP track siNC1_Veh_IP parent GR_ChIP-seq bigDataUrl MES661_141114_M00421_ABFD6.NC1-VehIP.1.sanger.cutAdapt.sickle.bowtie2_N1_hg19.filter.dedupe.merge.dedupe2.bs10_1xGenCov.bigwig shortLabel siNC1_Veh_IP longLabel siNC1 Veh GR IP UL3 type bigWig color 68,25,200 priority 1201 alwaysZero on graphTypeDefault bar maxHeightPixels 100:44:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on autoScale on viewLimits 0:50 visibility full # ################################## # bigWig coverage track # siNC1 Dex Input track siNC1_Dex_Input parent GR_ChIP-seq bigDataUrl MES661_141114_M00421_ABFD6.siH1-4DexInput.1.sanger.cutAdapt.sickle.bowtie2_N1_hg19.filter.dedupe.merge.dedupe2.bs10_1xGenCov.bigwig shortLabel siNC1_Dex_Input longLabel siNC1 1hr Dex Input UL3 type bigWig color 68,0,255 priority 1201 alwaysZero on graphTypeDefault bar maxHeightPixels 100:44:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on autoScale on viewLimits 0:50 visibility full # ################################## # bigWig coverage track # siH1.4 Veh GR IP track siNC1_Dex_IP parent GR_ChIP-seq bigDataUrl MES661_141114_M00421_ABFD6.NC1-DexIP.1.sanger.cutAdapt.sickle.bowtie2_N1_hg19.filter.dedupe.merge.dedupe2.bs10_1xGenCov.bigwig shortLabel siNC1_Dex_IP longLabel siNC1 1hr Dex GR IP UL3 type bigWig color 68,25,255 priority 1201 alwaysZero on graphTypeDefault bar maxHeightPixels 100:44:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on autoScale on viewLimits 0:50 visibility full # ################################## # bigWig coverage track # siH1.4 Veh Input track siH1e_Veh_Input parent GR_ChIP-seq bigDataUrl MES661_141114_M00421_ABFD6.siH1-4VehInput.1.sanger.cutAdapt.sickle.bowtie2_N1_hg19.filter.dedupe.merge.dedupe2.bs10_1xGenCov.bigwig shortLabel siH1e_Veh_Input longLabel siH1e Veh Input UL3 type bigWig color 0,200,60 priority 1201 alwaysZero on graphTypeDefault bar maxHeightPixels 100:44:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on autoScale on viewLimits 0:50 visibility full # ################################## # bigWig coverage track # siH1.4 Veh GR IP track siH1e_Veh_IP parent GR_ChIP-seq bigDataUrl MES661_141114_M00421_ABFD6.siH1-4VehIP.1.sanger.cutAdapt.sickle.bowtie2_N1_hg19.filter.dedupe.merge.dedupe2.bs10_1xGenCov.bigwig shortLabel siH1e_Veh_IP longLabel siH1e Veh GR IP UL3 type bigWig color 10,200,60 priority 1201 alwaysZero on graphTypeDefault bar maxHeightPixels 100:44:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on autoScale on viewLimits 0:50 visibility full # ################################## # bigWig coverage track # siH1.4 Dex Input track siH1e_Dex_Input parent GR_ChIP-seq bigDataUrl MES661_141114_M00421_ABFD6.siH1-4DexInput.1.sanger.cutAdapt.sickle.bowtie2_N1_hg19.filter.dedupe.merge.dedupe2.bs10_1xGenCov.bigwig shortLabel siH1e_Dex_Input longLabel siH1e 1hr Dex Input UL3 type bigWig color 0,255,20 priority 1201 alwaysZero on graphTypeDefault bar maxHeightPixels 100:44:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on autoScale on viewLimits 0:50 visibility full # ################################## # bigWig coverage track # siH1.4 Veh GR IP track siH1e_Dex_IP parent GR_ChIP-seq bigDataUrl MES661_141114_M00421_ABFD6.siH1-4DexIP.1.sanger.cutAdapt.sickle.bowtie2_N1_hg19.filter.dedupe.merge.dedupe2.bs10_1xGenCov.bigwig shortLabel siH1e_Dex_IP longLabel siH1e 1hr Dex GR IP UL3 type bigWig color 25,255,20 priority 1201 alwaysZero on graphTypeDefault bar maxHeightPixels 100:44:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on autoScale on viewLimits 0:50 visibility full #################################### ## track set ## NextSeq data for Kevin's ATAC seq Experiment track A1-2_ATACseq compositeTrack on shortLabel A1-2_ATACseq longLabel A1-2_ATAC-seq_NS50108 type bigWig allButtonPair on centerLabelsDense on dragAndDrop on priority 1200 alwaysZero on graphTypeDefault bar maxHeightPixels 100:44:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on autoScale on viewLimits 0:50 visibility full # ################################## # bigWig coverage track # A1-2 15min EtOH NFR coverage track 15minEtOH_NFR parent A1-2_ATACseq bigDataUrl trotterATACseq/A1-2EtOH15min.1.sanger.cutAdapt.fastq.sickle.fastq.bowtie2_N1_hg19.filter.NFR.dedupe.bs10_1xGenCov.bigwig shortLabel 15minEtOH_NFR longLabel A1-2 15 min EtOH NFR reads type bigWig color 115,82,68 priority 1201 alwaysZero on graphTypeDefault bar maxHeightPixels 100:44:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on autoScale on viewLimits 0:50 visibility full # ################################## # bigWig coverage track # A1-2 15min Dex NFR coverage track 15minDex_NFR parent A1-2_ATACseq bigDataUrl trotterATACseq/A1-2Dex15min.1.sanger.cutAdapt.fastq.sickle.fastq.bowtie2_N1_hg19.filter.NFR.dedupe.bs10_1xGenCov.bigwig shortLabel 15minDex_NFR longLabel A1-2 15 min Dex NFR reads type bigWig color 214,126,44 priority 1202 alwaysZero on graphTypeDefault bar maxHeightPixels 100:44:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on autoScale on viewLimits 0:50 visibility full # ################################## # bigWig coverage track # A1-2 30min EtOH NFR coverage track 30minEtOH_NFR parent A1-2_ATACseq bigDataUrl trotterATACseq/A1-2EtOH30min.1.sanger.cutAdapt.fastq.sickle.fastq.bowtie2_N1_hg19.filter.NFR.dedupe.bs10_1xGenCov.bigwig shortLabel 30minEtOH_NFR longLabel A1-2 30 min EtOH NFR reads type bigWig color 56,61,150 priority 1203 alwaysZero on graphTypeDefault bar maxHeightPixels 100:44:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on autoScale on viewLimits 0:50 visibility full # ################################## # bigWig coverage track # A1-2 30min Dex NFR coverage track 30minDex_NFR parent A1-2_ATACseq bigDataUrl trotterATACseq/A1-2Dex30min.1.sanger.cutAdapt.fastq.sickle.fastq.bowtie2_N1_hg19.filter.NFR.dedupe.bs10_1xGenCov.bigwig shortLabel 30minDex_NFR longLabel A1-2 30 min Dex NFR reads type bigWig color 70,148,73 priority 1204 alwaysZero on graphTypeDefault bar maxHeightPixels 100:44:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on autoScale on viewLimits 0:50 visibility full # ################################## # bigWig coverage track # A1-2 15min vs. 30min Dex NFR coverage track 15minVs30minDex_NFR parent A1-2_ATACseq bigDataUrl trotterATACseq/A1-2Dex_15minVs30min.bigwig shortLabel 15minVs30minDex longLabel A1-2 15min vs 30min Dex NFR reads type bigWig color 56,61,150 priority 1204 alwaysZero on graphTypeDefault bar maxHeightPixels 100:44:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on autoScale on viewLimits 0:50 visibility full