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Sample GSM605687 Query DataSets for GSM605687
Status Public on Feb 11, 2011
Title aly_floral-16-mRNA4
Sample type SRA
 
Source name floral tissue
Organism Arabidopsis lyrata
Characteristics strain: MN47
tissue: floral
developmental stage: stages 1-14
Growth protocol 16°C, 16 hour light period
Extracted molecule total RNA
Extraction protocol RNA was extracted from floral tissue (stages 1-14) using the Trizol(Invitrogen) RNA extraction protocol. rRNAs were depleted from 10 μg of RNA using the Ribominus kit (Invitrogen). Tobacco acid pyrophosphatase (Epicentre Biotechnologies) was used to remove the 5’ CAP, followed by metal ion fragmentation for 10 minutes at 70oC (RNA fragmentation kit, Ambion). The RNA was dephosphorylated using CIP, then size selected for fragments of 100-150 nt by PAGE. RNA was extracted from the gel by semi-dry electrotransfer to DE81 chromatography paper (Whatman), followed by salt elution. The Illumina 3’ and 5’ sRNA adapters were sequentially ligated with size selection and re-phosphorylation by PNK between ligations. Following a further cycle of PAGE size selection, the RNA was reverse transcribed with Fermentas Revertaid and PCR amplified for 15 cycles with Phusion DNA polymerase (Finnzymes) before sequencing (Illumina sequencing-by-synthesis).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer II
 
Data processing bed: We mapped mRNA-seq data to the A. lyrata genome using SHORE (http://shore.sourceforge.net)
 
Submission date Oct 07, 2010
Last update date May 15, 2019
Contact name Felix Ott
Organization name Max Planck Institute for Developmental Biology
Street address Spemannstr. 35-39
City Tuebingen
ZIP/Postal code 72076
Country Germany
 
Platform ID GPL11022
Series (2)
GSE24571 Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata [RNA-Seq]
GSE38113 Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata
Relations
SRA SRX031054
BioSample SAMN00120236

Supplementary file Size Download File type/resource
GSM605687_lyr-4_14.1.bed.gz 463.4 Mb (ftp)(http) BED
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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