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Series GSE162678 Query DataSets for GSE162678
Status Public on Dec 05, 2020
Title maize DDM1 targets RNA-directed DNA methylation on active chromatin
Organism Zea mays
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary In this work, we used chromatin immunoprecipitation coupled with high throughput sequencing (ChIP-seq) to ascertain the genome-wide occupancy of ZmDDM1 in maize genome. The results revealed that ZmDDM1 recognized an 8-bp-long GC-rich degenerate DNA sequence motif, which is enriched in transcription start sites (TSSs) and other euchromatic regions. Meanwhile, 24-nucleotide siRNAs and CHH methylation were delineated at the edge of ZmDDM1-occupied sites. ZmDDM1 could be co-purified with ZmAGO4 proteins, providing further evidence that ZmDDM1 is a component of RdDM complex in planta.
 
Overall design ZmDDM1 and ZmAGO4 ChIP-seq in maize developing embryo
 
Contributor(s) He Y, Long J
Citation(s) 33779761
Submission date Dec 04, 2020
Last update date Apr 08, 2021
Contact name Jincheng Long
E-mail(s) longjincheng1990@163.com
Phone +8613001298733
Organization name China Agricultural University
Department National Maize improvement center
Lab Yan He'Lab
Street address Hai Dian district ,Yuanmingyuan Road.Beijing
City Beijing
State/province Beijing
ZIP/Postal code 10083
Country China
 
Platforms (1)
GPL17628 Illumina HiSeq 2500 (Zea mays)
Samples (28)
GSM4956720 18DAP WT embryo ZmDDM1A ChIP-seq ChIP Rep1
GSM4956721 18DAP WT embryo ZmDDM1A ChIP-seq ChIP Rep2
GSM4956722 18DAP WT embryo ZmDDM1A ChIP-seq input Rep1
Relations
BioProject PRJNA682607
SRA SRP295916

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
GSE162678_H3K9me2_ChIP-seq_WT_Rep1_control_lambda.bedGraph.gz 705.9 Mb (ftp)(http) BEDGRAPH
GSE162678_H3K9me2_ChIP-seq_WT_Rep1_treat_pileup.bedGraph.gz 690.3 Mb (ftp)(http) BEDGRAPH
GSE162678_H3K9me2_ChIP-seq_WT_Rep2_control_lambda.bedGraph.gz 667.7 Mb (ftp)(http) BEDGRAPH
GSE162678_H3K9me2_ChIP-seq_WT_Rep2_treat_pileup.bedGraph.gz 559.9 Mb (ftp)(http) BEDGRAPH
GSE162678_IgG_ChIP-seq_WT_Rep1_control_lambda.bedGraph.gz 923.3 Mb (ftp)(http) BEDGRAPH
GSE162678_IgG_ChIP-seq_WT_Rep1_treat_pileup.bedGraph.gz 357.7 Mb (ftp)(http) BEDGRAPH
GSE162678_IgG_ChIP-seq_WT_Rep2_control_lambda.bedGraph.gz 962.0 Mb (ftp)(http) BEDGRAPH
GSE162678_IgG_ChIP-seq_WT_Rep2_treat_pileup.bedGraph.gz 324.1 Mb (ftp)(http) BEDGRAPH
GSE162678_WT_Rep1_cufflinks_genes.fpkm_tracking.gz 1.1 Mb (ftp)(http) FPKM_TRACKING
GSE162678_WT_Rep2_cufflinks_genes.fpkm_tracking.gz 1.1 Mb (ftp)(http) FPKM_TRACKING
GSE162678_ZmAGO4_ChIP-seq_WT_Rep1_peak.txt.gz 2.8 Mb (ftp)(http) TXT
GSE162678_ZmAGO4_ChIP-seq_WT_Rep2_peak.txt.gz 2.7 Mb (ftp)(http) TXT
GSE162678_ZmDDM1A_ChIP-seq_WT_Rep1_peak.txt.gz 1.2 Mb (ftp)(http) TXT
GSE162678_ZmDDM1A_ChIP-seq_WT_Rep2_peak.txt.gz 1.1 Mb (ftp)(http) TXT
GSE162678_ZmDDM1A_ChIP-seq_zmddm1a_Rep1_peak.txt.gz 21.3 Kb (ftp)(http) TXT
GSE162678_ZmDDM1A_ChIP-seq_zmddm1a_Rep2_peak.txt.gz 23.6 Kb (ftp)(http) TXT
GSE162678_ZmDDM1B_ChIP-seq_WT_Rep1_peak.txt.gz 1.4 Mb (ftp)(http) TXT
GSE162678_ZmDDM1B_ChIP-seq_WT_Rep2_peak.txt.gz 1.3 Mb (ftp)(http) TXT
GSE162678_ZmDDM1B_ChIP-seq_zmddm1b_Rep1_peak.txt.gz 43.4 Kb (ftp)(http) TXT
GSE162678_ZmDDM1B_ChIP-seq_zmddm1b_Rep2_peak.txt.gz 18.6 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data provided as supplementary file
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