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Series GSE128932 Query DataSets for GSE128932
Status Public on Mar 13, 2020
Title Arabidopsis retrotransposon virus-like-particles and their regulation by epigenetically activated small RNA
Organism Arabidopsis thaliana
Experiment type Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary We report polysomal RNA sequencing data (RNAseq), small RNAseq, and virus-like-particle (VLP) DNA sequencing (DNAseq) and ChIPseq data. Arabidopsis ddm1 mutants produce LTR retrotransposon transcripts that are processed into 21-22 nt easiRNAs by RNA-Dependent RNA polymerase 6 (RDR6). To test if 21-22 nt easiRNAs regulate transcription, translation and reverse transcription of LTR retrotransposons, we compared ddm1 and ddm1rdr6 in polysomal RNAseq, VLP DNAseq and ChIPseq data. We found a handful of ATHILA elements were differentially regulated in ddm1rdr6 for polysomal RNAseq, VLP DNAseq, and ChIPseq datasets. Using short read and long read technologies, we also profiled functional LTR retrotransposons that made full-length DNA by reverse transcription inside VLPs. Small RNAseq data were obtained in pollen and inflorescence tissues in wild-type and ddm1.
Overall design Polysomal RNAseq from total extract and microsome fraction with each 3 biological replicates of ddm1 and ddm1rdr6; Small RNAseq data from pollen and inflorescence tissues of wild-type and ddm1 with one replicate; VLP DNAseq using short read with 2-3 biological replicates and long read technologies with one replicate from wild-type, ddm1 and ddm1rdr6. ChIPseq was performed with 2 biological replicates from wild-type, rdr6, ddm1, and ddm1rdr6.
Contributor(s) Lee SC, Ernst E, Borges F, Berube B, Martienssen R
Citation(s) 32303559
Submission date Mar 27, 2019
Last update date Apr 30, 2020
Contact name Robert A Martienssen
Organization name Cold Spring Harbor Laboratory
Department Delbruck Bldg.
Lab Martienssen
Street address 1 Bungtown Rd
City Cold Spring Harbor
State/province NY
ZIP/Postal code 11724
Country USA
Platforms (4)
GPL13222 Illumina HiSeq 2000 (Arabidopsis thaliana)
GPL17970 Illumina MiSeq (Arabidopsis thaliana)
GPL19580 Illumina NextSeq 500 (Arabidopsis thaliana)
Samples (48)
GSM3688568 Total RNA ddm1 Rep 1
GSM3688569 Total RNA ddm1 Rep 2
GSM3688570 Total RNA ddm1 Rep 3
BioProject PRJNA529391
SRA SRP189599

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

Supplementary file Size Download File type/resource
GSE128932_RAW.tar 2.3 Gb (http)(custom) TAR (of BEDGRAPH, BW, TXT, VCF)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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