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Series GSE22252 Query DataSets for GSE22252
Status Public on Jun 21, 2010
Title Global identification of Arabidopsis thaliana ARGONAUTE1-associated small RNA.
Organism Arabidopsis thaliana
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary Small RNA from total RNA (input fraction) and immunoprecipitated HA-AGO1-complexes (IP fraction) were identified using high-throughput sequencing-by-synthesis.
 
Overall design Two replicate input fraction samples were used as controls for two replicate IP fraction samples. Total RNA from input fractions and small RNA that co-immunoprecipitated with HA-AGO1 complexes were size fractionated by polyacrylamide gel electrophoresis to recover 18-24 nucleotide small RNA. 3' and then 5' adaptors were serially ligated on to each small RNA followed by PAGE purification. RT-PCR was used to convert RNA to DNA amplicons. Amplicons were sequenced using the Illumina GAIIx platform. Resulting reads were parsed and mapped to the A. thaliana genome (TAIR9) using the CASHX pipeline.
 
Contributor(s) Cuperus JT, Carbonell A, Fahlgren N, Garcia-Ruiz H, Burke RT, Takeda A, Sullivan CM, Gilbert SD, Montgomery TA, Carrington JC
Citation(s) 20562854
Submission date Jun 09, 2010
Last update date Jan 05, 2016
Contact name James C Carrington
E-mail jcarrington@danforthcenter.org
Phone 314-587-1202
Organization name Donald Danforth Plant Science Center
Lab James C. Carrington
Street address 975 North Warson Road
City Saint Louis
State/province MO
ZIP/Postal code 63132
Country USA
 
Platforms (1)
GPL9302 Illumina Genome Analyzer II (Arabidopsis thaliana)
Samples (4)
GSM554062 smallRNA-total_RNA-rep1
GSM554063 smallRNA-total_RNA-rep2
GSM554064 smallRNA-HA_AGO1_IP-rep1
Relations
SRA SRP002667
BioProject PRJNA128651

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE22252_GFF_README.txt 1.4 Kb (ftp)(http) TXT
GSE22252_RAW.tar 35.1 Mb (http)(custom) TAR (of GFF)
Processed data provided as supplementary file

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