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Series GSE17339 Query DataSets for GSE17339
Status Public on Dec 31, 2009
Title High-throughput sequencing of small RNAs in Zea mays (maize)
Organism Zea mays
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from different maize tissues (including leaves, ears and tassels) collected from wild-type plants of the B73 variety. The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the maize genome under study.
 
Overall design Small RNA libraries were derived from leaves, ears and tassels of maize variety B73 (wild-type). Plants were grown in a flood irrigated plot at the University of Arizona (Tucson, AZ, USA) in 2007 and organs were pooled from several plants for each library. Young leaves were collected from 6-weeks-old seedlings. Post-meiotic immature ears were harvested from 10- and 11-week old plants while pre-meiotic tassels were collected from 8-week old plants. Total RNA was isolated using the Plant RNA Purification Reagent (Invitrogen) and submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. The small RNA libraries were sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina. PERL scripts were designed to remove the adapter sequences and determine the abundance of each distinct small RNA. We thank Lyudmila Sidorenko and Vicki Chandler for providing the plant material and Kan Nobuta for assistance with the computational methods.
 
Contributor(s) De Paoli E, Accerbi M, Green PJ, Meyers BC
Citation(s) 18815367, 19936048
Submission date Jul 27, 2009
Last update date May 15, 2019
Contact name Emanuele De Paoli
E-mail(s) emanuele.depaoli@gmail.com
Phone 00390432558676
Organization name University of Udine
Department Agricultural, Food, Environmental and Animal Sciences
Lab E. De Paoli
Street address via delle Scienze 206
City Udine
State/province UDINE
ZIP/Postal code 33100
Country Italy
 
Platforms (1)
GPL9361 Illumina Genome Analyzer II (Zea mays)
Samples (3)
GSM433620 Small RNAs from maize leaves
GSM433621 Small RNAs from maize ears
GSM433622 Small RNAs from maize tassels
This SubSeries is part of SuperSeries:
GSE28755 Comparative sequence analysis of plant small RNAs
Relations
SRA SRP001722
BioProject PRJNA141681

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Processed data included within Sample table
Raw data are available in SRA

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