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Sample GSM518430 Query DataSets for GSM518430
Status Public on May 14, 2010
Title A.lyrata_flowers-stage1-12_rep1
Sample type SRA
 
Source name flowers stage 1-12
Organism Arabidopsis lyrata
Characteristics strain: MN47
tissue: flowers
age: stage 1-12
Biomaterial provider Max Planck Campus Tübingen
Extracted molecule total RNA
Extraction protocol Small RNA were extracted from total RNA by size fractionation and converted to DNA amplicons by serial adaptor ligation to both ends followed by RT-PCR. DNA amplicons were sequenced using an Ilumina Genome Analyzer.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina Genome Analyzer
 
Description Wild type A. lyrata flower small RNA.
AL02
Data processing Small RNA sequences were parsed from Illumina sequencing data files through identification of the 3' adaptor boundary (the first six nucleotides of the 3' adaptor: CTGTAG). Only sequences that mapped perfectly to the A. thaliana (TAIR8; http://www.arabidopsis.org) or A. lyrata (v1.0; http://genome.jgi-psf.org/Araly1/Araly1.info.html ; http://www.phytozome.net/alyrata) genomes were included in the analysis.
********Raw data (fastq file) unavailable for this Sample********
 
Submission date Mar 05, 2010
Last update date Jun 11, 2013
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 GPL9180
Series (2)
GSE20660 MIRNA Gene Evolution in Arabidopsis lyrata and Arabidopsis thaliana: Illumina sequencing
GSE20662 MIRNA Gene Evolution in Arabidopsis lyrata and Arabidopsis thaliana
Relations
BioSample SAMN02196178

Data table header descriptions
SEQUENCE
COUNT RNA read count

Data table
SEQUENCE COUNT
TCTAAGGATGGCATAAGATGTAGA 1
GAAGAAAGTAGAATGTGTGCC 2
GGATGGTCTAAGATGTGTTTAAG 1
TGGATATGGCAGAAGTTTTTTGGA 4
CGAATTTTGGATCCCGTCATTTA 2
GAAGACGAACGAGATGGGTATA 24
CTAAAGACAGGATGCCTAGGCG 1
GATCTGATGAATGAGCTTACGGAA 1
AGCGTGGCAATCTTGTTAATAACA 1
TGTTCAGCGATATAGATAACGGAT 1
TACAAGACCCAATAGGATAAATA 1
GTAGTTTGACCGAGAGCAGTT 1
TGCTGCGGATTCACGGGCTCA 1
TGGTAGTCAGAAATGCAGGCGGT 1
GTTGGGGATGTAGCTCAGATGGTAGAGCGCT 1
AGAAGTGGGTACGTGTTGGAAGCG 41
TAGCAGTTGACGAGGAAGAATTAT 1
GACGGCAAACTTGGGAC 1
CGTCTCCATCGTCAGATTCTCA 1
ATACATCCCGATATAACTCTAAAA 1

Total number of rows: 1636295

Table truncated, full table size 41407 Kbytes.




Supplementary file Size Download File type/resource
GSM518430.gff3.gz 186.4 Mb (ftp)(http) GFF3
Processed data included within Sample table
Processed data provided as supplementary file

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