NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM3316505 Query DataSets for GSM3316505
Status Public on Feb 27, 2019
Title WT_rep3
Sample type SRA
 
Source name 3 weeks old plants
Organism Arabis alpina
Characteristics tissue: dissected shoot apices
genotype: wild-type
cultivar: Pajares
Growth protocol Plants are grown for 3 weeks at long day 16h light : 8 h dark.
Extracted molecule polyA RNA
Extraction protocol RNA was isolated using RNeasy Plant RNA isolation kit (Qiagen) according to manufacturer's instructions
The libraries were prepared from 1 µg total RNA with RNA integrity number >8 (Bioanalyzer; Agilent) using TruSeq type RNA kit (Illumina) at the Cologne Genome Centre and sequenced as 100-bp single-end reads on HiSeq2500 (Illumina) instrument.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing Filtered for per base Phred score greater than 25
Mapping of RNA-seq reads done by TopHat with default parameters
Expression Value was estimated by Cuffdiff considering all replicates
Differential gene expression analysis performed by Cuffdiff which uses t-test and pval calculation for each comparison
Adjustment of pval was done by Cuffdiff using  Benjamini-Hochberg method
Further analysis, like filtering on the basis of logFC and padj were performed by various application of Linux 
Genome_build: Arabis alpina V4 genome
Supplementary_files_format_and_content: excel files include RPKM values for each Sample
 
Submission date Aug 01, 2018
Last update date Feb 27, 2019
Contact name Maria Albani
Organization name University of Cologne
Department Botanical institute
Street address Carl-von-Linné-Weg 10
City Köln
ZIP/Postal code 50829
Country Germany
 
Platform ID GPL23515
Series (1)
GSE117977 The Arabis alpina APETALA2 orthologue delays flowering by repressing floral meristem identity genes during vernalization
Relations
BioSample SAMN09753066
SRA SRX4496259

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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