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Sample GSM707685 Query DataSets for GSM707685
Status Public on Apr 19, 2011
Title Two-step_purification_AGO1-associated_sRNAs_seedling
Sample type SRA
 
Source name TSP seedling
Organism Arabidopsis thaliana
Characteristics tissue: seedling
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 seedlings, 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
E-mail(s) hwang01@rockefeller.edu
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
Relations
SRA SRX058642
BioSample SAMN00260311

Supplementary file Size Download File type/resource
GSM707685_AGO1-TSP-seedling.txt.gz 5.6 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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