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Series GSE152971 Query DataSets for GSE152971
Status Public on Jun 25, 2020
Title Chromatin regulates expression of small RNAs to help maintain transposon methylome homeostasis in Arabidopsis
Organism Arabidopsis thaliana
Experiment type Non-coding RNA profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary We demonstrated that thousands of transposable elements (TEs) produce exceptionally high levels of siRNAs in Arabidopsis thaliana embryos.Depending on whether they are located in euchromatic or heterochromatic regions of the genome, bipartite-classified TEs generate siRNAs throughout embryogenesis according to two distinct patterns. siRNAs are transcribed in embryos and required to direct the re-establishment of DNA methylation on TEs from which they are derived in the new generation.
 
Overall design Examination of small RNAs and DNA methylation in Arabidopsis embryos and post embryonic tissues

Please note that each processed data generetated from all replicates is linked to the corresponding *Rep1 sample records.
 
Contributor(s) Nodine M, Papareddy R
Citation(s) 32943088, 34296996
Submission date Jun 22, 2020
Last update date Aug 18, 2021
Contact name Ranjith Papareddy
E-mail(s) ranjith.papareddy@gmi.oeaw.ac.at
Organization name Gregor Mendel Institute
Street address Dr Bohr Gasse 3
City Vienna
ZIP/Postal code 1030
Country Austria
 
Platforms (2)
GPL17639 Illumina HiSeq 2500 (Arabidopsis thaliana)
GPL24270 NextSeq 550 (Arabidopsis thaliana)
Samples (69)
GSM4630731 Sample 1_earlyHeart_Col0_Rep1.sRNA-seq
GSM4630732 Sample 2_earlyHeart_Col0_Rep2.sRNA-seq
GSM4630733 Sample 3_earlyHeart_Col0_Rep3.sRNA-seq
Relations
BioProject PRJNA641096
SRA SRP268298

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
GSE152971_RAW.tar 3.9 Gb (http)(custom) TAR (of BED, BW, TSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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