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Series GSE60141 Query DataSets for GSE60141
Status Public on May 25, 2016
Title A Comprehensive Atlas of Arabidopsis Regulatory DNA [DAP-seq]
Organisms Arabidopsis thaliana; Zea mays
Experiment type Other
Summary We have developed a high throughput, next-generation DNA sequencing assay for rapid transcription factor binding site (TFBS) discovery in a genomic context. DNA affinity purification sequencing (DAP-seq), which uses affinity-purified transcription factors (TFs) to capture genomic DNA fragments, was applied to all 1,725 Arabidopsis thaliana TFs. High confidence TFBS motifs for 529 TFs and genome-wide enrichment maps for 349 factors were identified. In total,~ 2.7 million TFBS were identified which predict thousands of TF target genes enriched for known and novel functions.. Comparison of TF-binding using cytosine-methylated and -unmethylated genomic DNA revealed a 2-50 fold inhibition at methylated motifs for ~82% (264) of factors tested while 4.6% (15) showed stronger binding to methylated motifs. Finally, we describe how binding of Arabidopsis and maize Auxin Response Factors (ARFs) at phased motif repeats is highly enriched at ARF target gene promoters and how this architecture may allow for stabilization of dimers/multimers.
 
Overall design Identification of sequence motifs for 530 transcription factors (529 Arabidopsis thaliana, 1 Zea mays) and genome-wide binding sites for 350 transcription factors (349 Arabidopsis thaliana, 1 Zea mays) by direct sequencing of affinity purified genomic DNA fragments. Idenfication of binding sites for 343 transcription factors (Arabidopsis thaliana) by direct sequencing of affinity purified, PCR amplified DNA libraries. Comparison to ChIP-Seq for ABI5 (AT2G36270).
The 530 transcription factors refer to the number of unique proteins assayed on non-amplified DNA libraries (i.e. "characteristics: DNA source" = "col" or "zm"). Additional 5 factors have only data on amplified libraries (i.e. "characteristics: DNA source = colamp"), which do not represent the natural DNA methylation state of the organism (therefore not counted; more details in the "description" field). A subset of 350 of the 530 have both motif and TFBS identification (i.e. "characteristics: subset = TFBS+motif"), and the rest 180 have only motif identification (i.e. "characteristics: subset = motif").
 
Contributor(s) O'Malley RC, Huang SC, Song L, Lewsey MG, Bartlett A, Galli M, Gallavotti A, Ecker JR
Citation(s) 27203113
Submission date Aug 06, 2014
Last update date May 15, 2019
Contact name Joseph R Ecker
E-mail(s) ecker@salk.edu
Phone 8584534100
Organization name HHMI-Salk-Institute
Department Genomic Analysis Laboratory
Lab Ecker lab
Street address 10010 North Torrey Pines Road
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
 
Platforms (2)
GPL17628 Illumina HiSeq 2500 (Zea mays)
GPL17639 Illumina HiSeq 2500 (Arabidopsis thaliana)
Samples (936)
GSM1924998 control_none.beads_col_v3a
GSM1924999 control_tnt-pixhalo_colamp_v3a
GSM1925000 ARF_ecoli-ZmARF5_col_4
This SubSeries is part of SuperSeries:
GSE60143 In vitro, genomic context identification of transcription factor binding sites
Relations
BioProject PRJNA257556
SRA SRP045296

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE60141_DAPSeq-AP2EREBP_tnt-At1g22810_col-chr1-5_GEM_events.narrowPeak.gz 65.4 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-AP2EREBP_tnt-At2g33710_col-chr1-5_GEM_events.narrowPeak.gz 92.5 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-AP2EREBP_tnt-At4g32800_col-chr1-5_GEM_events.narrowPeak.gz 63.7 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-AP2EREBP_tnt-ERF105_col-chr1-5_GEM_events.narrowPeak.gz 54.4 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-AP2EREBP_tnt-ERF15_col-chr1-5_GEM_events.narrowPeak.gz 159.5 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-AP2EREBP_tnt-ERF6_col-chr1-5_GEM_events.narrowPeak.gz 10.7 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-ARF_ecoli-MP_col-chr1-5_GEM_events.narrowPeak.gz 434.6 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-C2H2_tnt-At5g66730_col-chr1-5_GEM_events.narrowPeak.gz 35.9 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-C2H2_tnt-IDD5_col-chr1-5_GEM_events.narrowPeak.gz 4.3 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-C2H2_tnt-STZ_col-chr1-5_GEM_events.narrowPeak.gz 315.4 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-CPP_tnt-SOL1_col-chr1-5_GEM_events.narrowPeak.gz 130.8 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-G2like_tnt-At1g25550_col-chr1-5_GEM_events.narrowPeak.gz 184.3 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-G2like_tnt-At1g68670_col-chr1-5_GEM_events.narrowPeak.gz 154.6 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-G2like_tnt-At2g01060_col-chr1-5_GEM_events.narrowPeak.gz 167.4 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-HSF_tnt-HSFA6B_col-chr1-5_GEM_events.narrowPeak.gz 396.8 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-Homeobox_tnt-EDT1_col-chr1-5_GEM_events.narrowPeak.gz 31.7 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-Homeobox_tnt-PDF2_col-chr1-5_GEM_events.narrowPeak.gz 39.5 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-MYB_tnt-MYB44_col-chr1-5_GEM_events.narrowPeak.gz 244.0 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-MYB_tnt-MYB55_col-chr1-5_GEM_events.narrowPeak.gz 9.9 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-MYB_tnt-MYB60_col-chr1-5_GEM_events.narrowPeak.gz 9.4 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-MYB_tnt-MYB74_col-chr1-5_GEM_events.narrowPeak.gz 3.0 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-MYBrelated_tnt-EPR1_col-chr1-5_GEM_events.narrowPeak.gz 439.0 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-MYBrelated_tnt-LCL1_col-chr1-5_GEM_events.narrowPeak.gz 94.1 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-MYBrelated_tnt-TRP1_col-chr1-5_GEM_events.narrowPeak.gz 19.4 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-NAC_tnt-ANAC017_col-chr1-5_GEM_events.narrowPeak.gz 66.2 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-NAC_tnt-ANAC034_col-chr1-5_GEM_events.narrowPeak.gz 97.5 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-NAC_tnt-ANAC046_col-chr1-5_GEM_events.narrowPeak.gz 87.4 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-NAC_tnt-ANAC047_col-chr1-5_GEM_events.narrowPeak.gz 119.2 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-NAC_tnt-ANAC053_col-chr1-5_GEM_events.narrowPeak.gz 93.5 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-NAC_tnt-ANAC055_col-chr1-5_GEM_events.narrowPeak.gz 126.9 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-NAC_tnt-ANAC062_col-chr1-5_GEM_events.narrowPeak.gz 74.8 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-NAC_tnt-ANAC070_col-chr1-5_GEM_events.narrowPeak.gz 163.5 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-NAC_tnt-ANAC079_col-chr1-5_GEM_events.narrowPeak.gz 49.7 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-NAC_tnt-ANAC096_col-chr1-5_GEM_events.narrowPeak.gz 180.0 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-NAC_tnt-CUC2_col-chr1-5_GEM_events.narrowPeak.gz 60.2 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-NAC_tnt-NTL8_col-chr1-5_GEM_events.narrowPeak.gz 96.4 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-NAC_tnt-VND3_col-chr1-5_GEM_events.narrowPeak.gz 56.4 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-NAC_tnt-VND4_col-chr1-5_GEM_events.narrowPeak.gz 167.6 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-RAV_tnt-RAV1_col-chr1-5_GEM_events.narrowPeak.gz 186.2 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-TCP_tnt-At1g72010_col-chr1-5_GEM_events.narrowPeak.gz 39.4 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-TCP_tnt-TCP24_col-chr1-5_GEM_events.narrowPeak.gz 58.0 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-TCP_tnt-TCP3_col-chr1-5_GEM_events.narrowPeak.gz 26.1 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-Trihelix_tnt-At3g14180_col-chr1-5_GEM_events.narrowPeak.gz 110.7 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-WRKY_tnt-WRKY21_col-chr1-5_GEM_events.narrowPeak.gz 28.4 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-WRKY_tnt-WRKY22_col-chr1-5_GEM_events.narrowPeak.gz 350.5 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-WRKY_tnt-WRKY40_col-chr1-5_GEM_events.narrowPeak.gz 117.6 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-WRKY_tnt-WRKY70_col-chr1-5_GEM_events.narrowPeak.gz 129.6 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-WRKY_tnt-WRKY7_col-chr1-5_GEM_events.narrowPeak.gz 33.6 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-WRKY_tnt-WRKY8_col-chr1-5_GEM_events.narrowPeak.gz 314.2 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-bHLH_tnt-BIM2_colamp-chr1-5_GEM_events.narrowPeak.gz 411.5 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-bHLH_tnt-bHLH31_col-chr1-5_GEM_events.narrowPeak.gz 32.5 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-bHLH_tnt-bHLH34_col-chr1-5_GEM_events.narrowPeak.gz 15.6 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-bZIP_tnt-GBF3_col-chr1-5_GEM_events.narrowPeak.gz 99.1 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-bZIP_tnt-GBF3_colamp-chr1-5_GEM_events.narrowPeak.gz 160.2 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-bZIP_tnt-GBF6_col-chr1-5_GEM_events.narrowPeak.gz 156.7 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-bZIP_tnt-TGA1_col-chr1-5_GEM_events.narrowPeak.gz 66.4 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-bZIP_tnt-TGA2_col-chr1-5_GEM_events.narrowPeak.gz 40.5 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-bZIP_tnt-TGA3_col-chr1-5_GEM_events.narrowPeak.gz 59.0 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-bZIP_tnt-bZIP44_col-chr1-5_GEM_events.narrowPeak.gz 45.4 Kb (ftp)(http) NARROWPEAK
GSE60141_DAPSeq-bZIP_tnt-bZIP53_col-chr1-5_GEM_events.narrowPeak.gz 116.5 Kb (ftp)(http) NARROWPEAK
GSE60141_RAW.tar 77.3 Mb (http)(custom) TAR (of NARROWPEAK)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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