NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM578005 Query DataSets for GSM578005
Status Public on May 29, 2012
Title F2 hybrid replicate 2
Sample type SRA
 
Source name young seedlings aerial tissue
Organism Solanum lycopersicum x Solanum pennellii
Characteristics tissue: young seedlings aerial tissue
3'adapter: TCGTATGCCGTCTTCTGCTTGT
Treatment protocol Small RNAs were isolated from different lines of 2 week old Tomato seedlings.
Growth protocol Tomato seedlings were grown in Conviron growth chambers at 23'C, 60% RH and 16/8 light cycle in high nutrient compost.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Trizol (Invitrogen) and small RNA fraction was separated by PAGE gel. Adapter sequences appropriate for Illumina sequencing were ligated.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina Genome Analyzer
 
Data processing Sequence reads were obtained using the Illumina Genome Analyzer Pipeline. The 3 prime adaptor sequence was removed from the small RNA reads and the reads were aligned to the Tomato genome version bacs v340. Only reads with 100% match to the genome were retained.
 
Submission date Aug 11, 2010
Last update date May 15, 2019
Contact name Krys Kelly
Organization name University of Cambridge
Department Plant Sciences
Lab Baulcombe Group
Street address Downing Street
City Cambridge
ZIP/Postal code CB2 3EA
Country United Kingdom
 
Platform ID GPL10777
Series (1)
GSE23562 Small RNA profiling Tomato, wild tomato relative and series of introgression lines
Relations
SRA SRX026456
BioSample SAMN00110633

Supplementary file Size Download File type/resource
GSM578005_SL367.v_Solanum_lycopersicon_genome-bacsv340.patman.aligned_reads.fasta.gz 5.6 Mb (ftp)(http) FASTA
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap