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Series GSE28591 Query DataSets for GSE28591
Status Public on Apr 19, 2011
Title Characterization of AGO1-/AGO4-associated smRNAs
Organism Arabidopsis thaliana
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary To fully characterize smRNAs associated with AGO1 and AGO4, we developed a two-step protocol to purify AGO/smRNA complexes from flowers, leaves, roots and seedlings with enhanced purity, and sequenced the smRNAs by Illumina’s technology. We identified some additional miRNAs, collateral miRNAs encoded in known miRNA precursors, phased smRNA clusters and nat-siRNAs. Organ specific sequencing provided digital expression profiles of all obtained smRNAs, especially miRNAs.
Overall design We used extracts from Arabidopsis flowers, leaves and roots as well as ten-day old seedlings to purify smRNAs associated with AGO1 and AGO4 protein complexes using a two-step immunoprecipitation method.
Contributor(s) Wang H, Zhang X, Liu J, Kiba T, Woo J, Ojo T, Hafner M, Tuschl T, Chua N, Wang X
Citation(s) 21457371
Submission date Apr 13, 2011
Last update date May 15, 2019
Contact name Huan Wang
Organization name The Rockefeller University
Lab Chua Nam-Hai
Street address 1230 York Avenue
City New York
State/province New York
ZIP/Postal code 10065
Country USA
Platforms (1)
GPL9302 Illumina Genome Analyzer II (Arabidopsis thaliana)
Samples (14)
GSM707678 WT-flower
GSM707679 WT-leaf
GSM707680 WT-root
SRA SRP006477
BioProject PRJNA139119

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE28591_RAW.tar 158.3 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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