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Sample GSM614641 Query DataSets for GSM614641
Status Public on Jan 12, 2011
Title Ler x C24 F1 hybrid - Whole 2-week old seedlings Rep1
Sample type SRA
 
Source name Whole 2-week old seedlings
Organism Arabidopsis thaliana
Characteristics ecotype: Ler x C24 F1 hybrid
tissue: whole seedlings
age: 2-weeks old
Growth protocol All plants were grown at 23C under a 16-hour light/8-hour dark cycle.
Extracted molecule total RNA
Extraction protocol 14 to 15 day old seedlings were collected, pooled and RNA extracted using trizol (Ambion). RNA underwent 1 chloroform step before being precipitated in isopropanol over night at minus 20 degrees. Total RNA was washed once in 75% ethanol before being resuspended in DEPC treated water. Total RNA was stored at -80oC before being sent to Geneworks (Adeliade, Australia) where the RNA underwent standard illumina small RNA preparation and sequencing.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina Genome Analyzer
 
Description small RNA
Data processing RNA-seq reads were mapped to Arabidopsis genome (Tair 8) using Novoalign version 2.10 from NovoCraft Technologies (www.novocraft.com) with '-a' (adaptor stripping) invoked.
 
Submission date Oct 29, 2010
Last update date May 15, 2019
Contact name Michael Groszmann
Organization name CSIRO
Department Agriculture
Lab Program X
Street address Clunies Ross St
City Acton
State/province ACT
ZIP/Postal code 2601
Country Australia
 
Platform ID GPL9062
Series (1)
GSE25022 sRNA populations of 2 week old seedlings from Arabidopsis ecotypes C24, Ler, and their two reciprocal F1 hybrids
Relations
SRA SRX029681
BioSample SAMN00116905

Supplementary file Size Download File type/resource
GSM614641_LerxC24_raw_read_mapping_novoalign_output.nv.txt.gz 121.6 Mb (ftp)(http) TXT
GSM614641_LerxC24_uniquely_mapped.bed.gz 4.2 Mb (ftp)(http) BED
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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