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Series GSE150435 Query DataSets for GSE150435
Status Public on Feb 10, 2021
Title RNA-seq for Col-0 WT, ddm1(-/-) and Col-0 X ddm1 (F1) to evaluate transposon expression in F1 Col-0Xddm1 and ddm1
Organism Arabidopsis thaliana
Experiment type Expression profiling by high throughput sequencing
Summary Silencing of transposons by the chromatin remodeler DDM1 is mediated by the deposition of heterochromatic H2A variants.
Transposon mobility and silencing participates in genome evolution but also threaten genome integrity. DECREASED DNA METHYLATION 1 (DDM1) belongs to a conserved family of chromatin remodelers that are required to silence transposons, yet the underlying molecular mechanism has remained unknown. Here we show that DDM1 binds the histone variant H2A.W through two conserved domains that are required to deposit H2A.W and maintain transposon silencing. The mechanism of transcriptional silencing described here is likely shared among chromatin remodelers of the DDM1 family and heterochromatic H2A variants that have evolved in mammals.
 
Overall design Total RNA was extracted with Spectrum plant total RNA kit (Sigma Aldrich) from 4-5 week old leaves of WT Col-0, F1 DDM1/ddm1 (Col-0Xddm1) and ddm1 2nd generation. For RNA-seq analyses, rRNA was removed by Ribo-Zero rRNA Removal kit (Illumina). After depletion of rRNA, RNA-seq libraries were generated with NEBNext UltraII directional RNA library prep kit for Illumina (New England Biolabs) following the manufacturer’s instructions. The libraries were sequenced with Illumina Hiseq 2500 to generate single-end 50 bp reads. Samples were prepared from three independent biological replicates.
 
Contributor(s) Jamge B, Osakabe A
Citation(s) 33833428
Submission date May 12, 2020
Last update date Apr 20, 2021
Contact name Bhagyshree Babasaheb Jamge
E-mail(s) bhagyshree.jamge@gmi.oeaw.ac.at
Organization name Gregor Mendel Institute
Street address Dr. Bohr Gasse -3
City Vienna
ZIP/Postal code 1030
Country Austria
 
Platforms (1)
GPL17639 Illumina HiSeq 2500 (Arabidopsis thaliana)
Samples (9)
GSM4550586 Col-0 Rep1
GSM4550587 Col-0 Rep2
GSM4550588 Col-0 Rep3
This SubSeries is part of SuperSeries:
GSE150436 The chromatin remodeler DDM1 silences transposons through deposition of the histone variant H2A.W
Relations
BioProject PRJNA632034
SRA SRP261342

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Supplementary file Size Download File type/resource
GSE150435_RAW.tar 3.3 Mb (http)(custom) TAR (of TSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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