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Series GSE98408 Query DataSets for GSE98408
Status Public on Jul 20, 2017
Title Conservation and divergence of small RNA pathways in vascular plants revealed by small RNA analyses in lycophytes and ferns
Organisms Psilotum nudum; Pteris vittata; Lygodium japonicum; Cibotium barometz; Diplazium esculentum; Vandenboschia striata; Asplenium nidus; Odontosoria chinensis; Salvinia cucullata; Microlepia platyphylla; Azolla caroliniana; Ophioglossum vulgatum; Palhinhaea cernua; Selaginella moellendorffii; Plenasium vachellii; Salvinia molesta; Microsorum cuspidatum; Equisetum ramosissimum; Alsophila spinulosa; Cyrtomium fortunei; Isoetes sinensis; Selaginella uncinata; Angiopteris fokiensis; Dicranopteris pedata; Diplopterygium chinense
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary Pathways underlying miRNA biogenesis, degradation, and activity were established early in land plant evolution, but the 24-nt siRNA pathway that guides DNA methylation was incomplete in early land plants, especially lycophytes. We show that the functional diversification of key gene families such as DICER-LIKE and ARGONAUTE (AGO) as observed in angiosperms occurred early in land plants followed by parallel expansion of the AGO family in ferns and angiosperms. We uncovered an unexpected AGO family specific to lycophytes and ferns. Our phylogenetic analyses of miRNAs in lycophytes, bryophytes, ferns, and angiosperms refined the temporal origination of conserved miRNA families in land plants.
 
Overall design Examine the 19-26 nt small RNA in 25 samples from 4 lycophytes and 21 ferns, and the degradome of S. moellendorffii fronds.
 
Contributor(s) Chen X
Citation(s) 28835265
Submission date May 01, 2017
Last update date Jul 25, 2021
Contact name Chenjiang You
E-mail(s) chenjiang.you@ucr.edu, youchenjiang2003@hotmail.com
Organization name Fudan University
Street address 2005 Songhu Rd
City Shanghai
State/province Shanghai
ZIP/Postal code 200438
Country China
 
Platforms (25)
GPL23398 Illumina HiSeq 2500 (Selaginella uncinata)
GPL23399 Illumina HiSeq 2500 (Selaginella moellendorffii)
GPL23400 Illumina HiSeq 2500 (Isoetes sinensis)
Samples (26)
GSM2594392 Sun_sRNA
GSM2594393 Smo_sRNA
GSM2594394 Isi_sRNA
Relations
BioProject PRJNA385013
SRA SRP105811

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
GSE98408_RAW.tar 459.2 Mb (http)(custom) TAR (of FASTA)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
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