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Sample GSM429420 Query DataSets for GSM429420
Status Public on Apr 12, 2010
Title 454-sequenced P19 silencing suppressor mutant Cymbidium Ringspot Virus (Cym19stop)-derived siRNAs
Sample type SRA
 
Source name Early systemic leaves of Cym19stop-infected Nicotiana benthamiana
Organisms Nicotiana benthamiana; Cymbidium ringspot virus
Characteristics tissue: early systemic leaves
treatment: Cym19stop infection
Growth protocol 3 weeks old Nicotiana benthamiana plants grown in soil under normal growth conditions were used for virus infection. After infection with Cym19stop, plants were grown in fitotrons under a 14 h light (50 E µm-2s-1) and 10 h dark regime at 21°C
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from early systemic leaves of Nicotiana benthamiana infected with Cym19stop. The homogenized plant materials were resuspended in 600 \u03bcL of extraction buffer (0.1 M glycine-NaOH, pH 9.0, 100 mM NaCl, 10 mM EDTA, 2% SDS, and 1% sodium lauroylsarcosine) and mixed with an equal volume of phenol. The aqueous phase was treated with equal volumes of phenol and chloroform, precipitated with ethanol, and resuspended in sterile water and used in subsequent reactions.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model 454 GS
 
Description Cym19stop-derived small RNAs from early systemic leaves of Nicotiana benthamiana.
Data processing Removed adaptors. Sequences without adapters were discarded. Small RNA sequences were mapped to the CymRSV genome (GenBank: X15511.1).
 
Submission date Jul 17, 2009
Last update date Jun 11, 2013
Contact name Simon Moxon
E-mail(s) simonm@cmp.uea.ac.uk
Organization name University of East Anglia
Street address University of East Anglia
City Norwich
State/province Norfolk
ZIP/Postal code NR4 7TJ
Country United Kingdom
 
Platform ID GPL15026
Series (2)
GSE17164 Structural and Functional Analysis of Viral siRNAs using 454 sequencing
GSE17278 Structural and Functional Analysis of Viral siRNAs
Relations
BioSample SAMN02198688

Data table header descriptions
SEQUENCE small RNA sequence (DNA form)
COUNT number of times small RNA was sequenced

Data table
SEQUENCE COUNT
AAAAAAAAAAAAAAAAAAAAGACGTCACGC 1
AAAAAAAAAAAAAAAATAGTTGGGATGGA 1
AAAAAAAAAAAAAACTACGACA 1
AAAAAAAAAAAAAATAGACTTGAAC 1
AAAAAAAAAAAAAATGCTCC 1
AAAAAAAAAAAAAATTAATCCGGA 1
AAAAAAAAAAAAAATTAGCTGTC 1
AAAAAAAAAAAAACTAACCCTAAGCACA 1
AAAAAAAAAAAAACTACCCTAACGCACA 1
AAAAAAAAAAAAACTACTCCACAGCTCG 1
AAAAAAAAAAAAACTAGGTTGC 1
AAAAAAAAAAAAAGGAAAAGAAACAAAA 1
AAAAAAAAAAAAATAACTACTC 1
AAAAAAAAAAAAATAAGTCATCTGA 1
AAAAAAAAAAAAATTAAGGGAACAAGC 1
AAAAAAAAAAAAATTTGACTGGGT 1
AAAAAAAAAAAACAAGCACA 1
AAAAAAAAAAAACTACTATTTTCCC 1
AAAAAAAAAAAAGTACACCTTTAGACG 1
AAAAAAAAAAAATTCTCA 1

Total number of rows: 38444

Table truncated, full table size 973 Kbytes.




Supplementary file Size Download File type/resource
GSM429420.fna.gz 2.0 Mb (ftp)(http) FNA
GSM429420.qual.gz 4.4 Mb (ftp)(http) QUAL
Raw data provided as supplementary file
Processed data included within Sample table

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