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Series GSE173426 Query DataSets for GSE173426
Status Public on Apr 28, 2021
Title Nuclear and cytoplasmic RNA exosomes and PELOTA limit miRNA-induced secondary siRNA production
Organism Arabidopsis thaliana
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary In this study, we aim at understanding which RNA degradation pathways are involved in keeping the secondary siRNA production in check in Arabidopsis thaliana. We have sequenced small RNAs from various T-DNA insertation single mutants and compared their capability of producing ectopic secondary siRNAs from endogenous miRNA targets. The mutants used in the work stem from three library pools from three different experiments. Libraries from all three experiments are submitted together here. The experiments can be distinguished by their title and their tag:experiment. There is a matrix of normalized reads from each pool of library as well called normalizedExp1.txt, normalizedExp2.txt and normalizedExp3.txt
 
Overall design Libraries Exp.1: small RNA seq data from three mutant lines (ski2-5, ski3-5, cer7-3) and a wild type line. All lines are ecotype Col-0. There are technical replicates of each sample. Libraries in Exp.2: small RNA seq data from 6 mutant lines (ski2-5, pel1-1, pel1-2, hen2-5, rrp4, rrp45a) and a wild type line. All lines are ecotype Col-0. There are three biological triplicates of each sample except for pel1-1 that does not have a replicate. Libraries in Exp.3: small RNA seq data from three mutant lines (ski2-5, hen2-4, sop1-5) and a wild type line. All lines are ecotype Col-0. There are biological triplicates of each sample.
 
Contributor(s) Vigh ML, Brodersen P, Thieffry A, Arribas-Hernandéz L
Citation(s) 35037064
Submission date Apr 27, 2021
Last update date Mar 03, 2022
Contact name Peter Brodersen
E-mail(s) pbrodersen@bio.ku.dk
Organization name University of Copenhagen
Department Department of Biology
Lab Peter Brodersen Lab
Street address Ole Maaløes Vej 5
City København N
ZIP/Postal code 2200
Country Denmark
 
Platforms (1)
GPL19580 Illumina NextSeq 500 (Arabidopsis thaliana)
Samples (39)
GSM5267560 Col-0 WT R1 Exp1
GSM5267561 Col-0 WT R2 Exp1
GSM5267562 cer7-3 R1 Exp1
Relations
BioProject PRJNA725493
SRA SRP316571

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
GSE173426_deseqcontrast1.xlsx 23.5 Mb (ftp)(http) XLSX
GSE173426_deseqcontrast2.xlsx 49.7 Mb (ftp)(http) XLSX
GSE173426_deseqcontrast3.xlsx 25.2 Mb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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