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Sample GSM707682 Query DataSets for GSM707682
Status Public on Apr 19, 2011
Title Two-step_purification_AGO1-associated_sRNAs_flower
Sample type SRA
Source name TSP flower
Organism Arabidopsis thaliana
Characteristics tissue: flower
smrna: AGO1-associated small RNAs
Growth protocol Flowers were collected from 6-week-old plants grown on soil in a growth chamber under 12 hr light/12 hr dark at 21°C. Leaves and roots were harvested from 4-week-old plants grown hydroponically under 12 hr light/12 hr dark at 21°C in the MGRL medium. Seedlings were grown on MS plates in a growth chamber under 16 hr light/8 hr dark at 21°C.
Extracted molecule total RNA
Extraction protocol For two-step purification of AGO/smRNA complexes, cleared extracts were fractioned on Superdex 200 10/300 columns (Akta-FPLC, GE) and further immunoprecipitated. After size-fractionation, total RNA or RNA recovered from the purified AGO-smRNA complexes were ligated to 3'² adapter (AppTCGTATGCCGTCTTCTGCTTG-L) and 5'² adapter (rGrUrUrCrArGrArGrUrUrCrUrArCrArGrUrCrCrGrArCrGrArUrC) sequentially. The ligated products were amplified by RT-PCR and used for Illumina's deep sequencing.
Library strategy RNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina Genome Analyzer II
Description smRNA sequencing data of AGO1-associated smRNAs in flowers, two-step purification
Data processing Adapters were removed by Perl script, if a hit with at most 1 mismatch to the first 4-nt of the adapter sequence could be found. After adapter removal, only 19-28 nt reads were aligned to the Arabidopsis thaliana genome (TAIR9) using C program. The small RNAs with perfect genomic matches are used for further analysis.
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
Platform ID GPL9302
Series (1)
GSE28591 Characterization of AGO1-/AGO4-associated smRNAs
SRA SRX058639
BioSample SAMN00260308

Supplementary file Size Download File type/resource
GSM707682_AGO1-TSP-flower.txt.gz 7.2 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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