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Series GSE108490 Query DataSets for GSE108490
Status Public on Jan 29, 2020
Title Genome-wide profiling of EDM3 dependent H3K9me2 in Arabidopsis thaliana
Organism Arabidopsis thaliana
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary We perform genome-wide profiling of H3K9me2 in the Arabidopsis thaliana edm3 mutant. By var-seq, we identified EDM3 as a nuclear-localized protein featuring a single RNA-recognition motif (RRM). Similar to PHD finger-containing histone binding protein EDM2, EDM3 promotes high levels of H3K9me2 at RPP7 and controls transcripts of this NLR gene by suppressing proximal polyadenylation and promoting the synthesis of full-length RPP7-coding mRNAs. Our results showed that EDM3 affects levels of this epigenetic mark at a set of genes and transposons, the vast majority of which also feature EDM2-dependent H3K9me2.
Overall design H3K9me2 ChIP-seq profiling in edm3 and wild-type Col5 with two replicates respectively, var-seq for edm3 and wild-type Col5
Contributor(s) Lai Y, Lu XM, Katiyar N, Le Roche K, Eulgem T
Citation(s) 30407670
Submission date Dec 24, 2017
Last update date Mar 03, 2020
Contact name Xueqing Maggie Lu
Phone 8186878070
Organization name University of California, Riverside
Department Cell Biology
Lab Le Roch
Street address 3401 Watkins Drive, Genomics, Room 2126
City Riverside
State/province CA
ZIP/Postal code 92521
Country USA
Platforms (2)
GPL17970 Illumina MiSeq (Arabidopsis thaliana)
GPL19580 Illumina NextSeq 500 (Arabidopsis thaliana)
Samples (10)
GSM2901575 H3K9me2_WT_Rep1
GSM2901576 H3K9me2_WT_Rep2
GSM2901577 H3K9me2_edm3_Rep1
BioProject PRJNA427433
SRA SRP127503

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Supplementary file Size Download File type/resource
GSE108490_RAW.tar 4.3 Gb (http)(custom) TAR (of BED, TXT)
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Processed data provided as supplementary file
Raw data are available in SRA

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