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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
Other
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
E-mail(s) maggieqqlu@gmail.com
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
Relations
BioProject PRJNA427433
SRA SRP127503

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
GSE108490_RAW.tar 4.3 Gb (http)(custom) TAR (of BED, TXT)
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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