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Series GSE35254 Query DataSets for GSE35254
Status Public on Apr 03, 2012
Title High-throughput Illumina Hiseq2000 seuqencing of small RNAs from Hevea brasiliensis PB260 and PB217 clones
Organism Hevea brasiliensis
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary MicroRNAs (miRNAs) are non-coding, short, single-stranded RNAs with essential roles in gene regulation in various organisms including higher plants. In contrast to the vast information on miRNAs from many economically important plants, almost nothing has been reported on the identification or analysis of miRNAs from rubber tree (Hevea brasiliensis L.), the most important natural rubber-producing crop. To identify miRNAs and their target genes in rubber tree, high throughput sequencing combined with a computational approach was performed. Four small RNA libraries were constructed for deep sequencing from mature and young leaves of two rubber tree clones, PB 260 and PB 217, which provide high and low latex yield, respectively. 237 miRNAs belonging to 37 known miRNA families were identified, and northern hybridization validated miRNA expression and revealed developmental stage-dependent and clone-specific expression for some miRNAs. We took advantage of the newly released rubber tree genome assembly as well as the genomic databases from leafy spurge and cassava, two species related to rubber tree, and predicted 15 novel miRNAs.
 
Overall design 4 samples examined: PB260 mature leaves, PB260 young leaves, PB217 mature leaves, and PB217 young leaves.
 
Contributor(s) Narangajavana J, Chen X, Lertpanyasampatha M, Gao L
Citation(s) 22407387
Submission date Jan 20, 2012
Last update date May 15, 2019
Contact name Lei Gao
E-mail(s) leigao@szu.edu.cn
Organization name shenzhen university
Department College of Life Sciences
Street address Nanhai Ave 3688
City shenzhen
State/province guangdong
ZIP/Postal code 518060
Country China
 
Platforms (1)
GPL11409 Illumina HiSeq 2000 (Hevea brasiliensis)
Samples (4)
GSM864552 Endogenous small RNAs from Hevea brasiliensis, PB217, mature leaves
GSM864553 Endogenous small RNAs from Hevea brasiliensis, PB217, young leaves
GSM864554 Endogenous small RNAs from Hevea brasiliensis, PB260, mature leaves
Relations
SRA SRP010464
BioProject PRJNA152819

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Supplementary file Size Download File type/resource
GSE35254_RAW.tar 28.6 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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