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Series GSE98141 Query DataSets for GSE98141
Status Public on Jul 22, 2017
Title Genome-wide identification and characterization of novel lncRNAs in Arabidopsis thaliana
Organism Arabidopsis thaliana
Experiment type Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
Summary To explore the overall long noncoding RNA (lncRNA) involved in growth and development of Arabidopsis thaliana across the lifespan, we deeply sequenced samples of whole plants from different developmental stages (4 rosette leaves>1mm, 14 rosette leaves>1mm, rosette growth complete, first flower buds visible, flourishing florescence, first silique shattered, senescence) using strand-specific RNA sequencing (ssRNA-seq) menthod. We obtained 28.8 Gb raw data and identified 156 novel lncRNAs (unreported in all public plant lncRNA databases) . We also categorized the novel lncRNAs as intergenic, intronic, antisense, overlapped with perhaps pseudogenes and mRNA based on their location on the Arabidopsis genome. Furthermore, lncRNAs targeted protein-coding genes were predicted and functional annotated. In addition, we constructed a network of interactions between ncRNAs (miRNAs, lncRNA) and mRNAs. Our results suggest that the identified novel lncRNAs are important in modulating development process of Arabidopsis, and provide a rich resource for further research on the function of these novel lncRNAs.
 
Overall design RNA-sequencing of whole plants at 7 developmental stages (pooled sample).
 
Contributor(s) Jin B, Lu Z
Citation(s) 28499866
Submission date Apr 24, 2017
Last update date Jul 25, 2021
Contact name Biao Jin
E-mail(s) bjin@yzu.edu.cn
Phone 13056359569
Organization name Yangzhou University
Department College of Horticulture and Plant Protection
Lab Jin Lab
Street address Wenhui east road no. 48
City Yangzhou
State/province Jiangsu
ZIP/Postal code 225009
Country China
 
Platforms (1)
GPL13222 Illumina HiSeq 2000 (Arabidopsis thaliana)
Samples (1)
GSM2588471 Ath_lncRNA
Relations
BioProject PRJNA384090
SRA SRP105133

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
GSE98141_RAW.tar 10.0 Kb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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