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Sample GSM304283 Query DataSets for GSM304283
Status Public on Aug 16, 2008
Title HA-AGO2 Co-IP Fraction Small RNA
Sample type RNA
 
Source name Inflorescence tissue: flower stages 1-12
Organism Arabidopsis thaliana
Characteristics Col-0 ecotype transformed with AGO2:HA-AGO2
Growth protocol Transgenic plants were grown on MS medium containing hygromycin (50 ug/ml) for 7 days, transferred to soil, and maintained in a standard greenhouse with 16 hr light/8 hr dark supplemental light cycle.
Extracted molecule total RNA
Extraction protocol Inflorescence tissue (flower stages 1-12) from zip-1 AGO7:HA-AGO7- or Col-0 AGO2:HA-AGO2-transformed plants was ground in lysis buffer. Cell debris was removed by centrifugation for 10 min at 12,000 g and the supernatant was partitioned into input and immunoprecipitation fractions. RNA was isolated immediately from the input fraction by phenol/chloroform extraction, followed by ethanol precipitation. HA-AGO7 and HA-AGO2 were immunoprecipitated using HA antibody and Protein A agarose beads. Beads were treated with proteinase K. RNA was isolated from the supernatant. Small RNA were fractionated on denaturing 17% polyacrylamide gels. Amplicons for sequencing were prepared by 5’ and 3’ adaptor ligations followed by RT-PCR. Sequencing-by-synthesis was done using an Illumina 1G Genome Analyzer.
Label not applicable
Label protocol not applicable
 
Hybridization protocol not applicable
Scan protocol not applicable
Description HA-AGO2 Co-IP Fraction Small RNA
Data processing Small RNA sequences were parsed from Illumina sequencing data files through identification of adaptor boundaries. Only sequences that mapped to the Arabidopsis thaliana Col-0 genome were included in the analysis.
 
Submission date Jul 08, 2008
Last update date Aug 15, 2008
Contact name James C Carrington
E-mail(s) 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
 
Platform ID GPL7029
Series (1)
GSE12037 ARGONAUTE-small RNA Interactions in Arabidopsis thaliana Identified by High-Throughput Sequencing

Data table header descriptions
ID_REF SEQUENCE
VALUE NUMBER OF READS

Data table
ID_REF VALUE
AAAAAAAAAGATTGAGCGTGA 2
AAAAAAAAGGTGAATCTGA 3
AAAAAAAATTGTTGCCGTTGG 29
AAAAAAAATTGTTGCCGTTGGG 43
AAAAAAACTTTGATTGTGTTT 1
AAAAAAAGGATCATGGTCGTG 1
AAAAAAATGGGAGATGTCCGGA 2
AAAAAAATGGGTCGGGTTGTTTCA 1
AAAAAAATTGGTTGTAGGGGA 2
AAAAAAATTGTTGCCGTTGG 7
AAAAAAATTGTTGCCGTTGGG 329
AAAAAAATTGTTGCCGTTGGGG 36
AAAAAAATTGTTGCCGTTGGGGAA 1
AAAAAACAGTCTGATCCGTTGATG 3
AAAAAACCGTCAGCTTTGGTCAGA 1
AAAAAACCTGATTGTTCTGAGACT 2
AAAAAACCTGCTGGTCCTCACCGA 2
AAAAAACGCTGAGAAGTTGCCA 1
AAAAAACGTTTGTTTGGCGCG 1
AAAAAACTACGGTTGGAGTTGG 16

Total number of rows: 207572

Table truncated, full table size 5027 Kbytes.




Supplementary file Size Download File type/resource
GSM304283_AGO2_IP_Eland.txt.gz 107.7 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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