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Sample GSM595273 Query DataSets for GSM595273
Status Public on Jun 01, 2011
Title total amplified RNA, globular Ler/Col embryos, sample # LerCol_4
Sample type SRA
 
Source name embryos (dissected)
Organism Arabidopsis thaliana
Characteristics Stage: globular embryo stage with suspensor (partial)
maternal strain: Landsberg erecta (Ler)
maternal genotype/variation: wildtype
paternal strain: Columbia_0 (Col0)
maternal genotype/variation: wildtype
Growth protocol Plants were grown under 16h light.
Extracted molecule total RNA
Extraction protocol 1-RNA extraction: PicoPure RNA Isolation Kit (Arcturus). 2-RNA amplification: WT-Ovation™ Pico RNA Amplification System (NuGEN Technologies, USA) producing single-stranded cDNA. 3- Second strand synthesis: poly-A tails added using Terminal Transferase (New England Biolabs, USA) in presence of dATPs (1 PCR cycle using Ex Taq Polymerase , (TaKaRa, Japan), and oligo(dT)12-18 primers (Invitrogen). 4-Library preparation: from 500 ng ds cDNA, Covaris S2 system (Covaris, Inc.), sheared into 80–130 bp fragments , DNA ends were repaired and ligated to SOLiD P1 and P2 adaptors, followed by enrichment by PCR (7 cycles) and a size selection on gel
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model AB SOLiD System 3.0
 
Description linear amplified
Data processing 50 base reads generated by SOLiD v3 were aligned to the TAIR8.0 version of the Arabidopsis Col genome using the SOLiD™ System Analysis Pipeline Tool (Corona Lite 4.0r2.0, Applied Biosystems, USA), allowing up to 4 color-space mismatches with the additional rule “count valid adjacent errors as single errors”. For transcriptome profiles, reads were excluded if they mapped to more than one genomic position, mapped at splice junctions or were partially overlapping. Consequently, full-length reads uniquely mapping inside a transcript were taken.
Processed data file contains transcript coverage, read count (full-length), transcript type
 
Submission date Sep 17, 2010
Last update date May 15, 2019
Contact name Marc William Schmid
E-mail(s) contact@mwschmid.ch
Organization name MWSchmid GmbH
Street address Hauptstrasse 34
City Glarus
ZIP/Postal code 8750
Country Switzerland
 
Platform ID GPL10088
Series (1)
GSE24198 Deep-sequencing of total RNA from manually dissected wild-type and kyp-2m/KYPp Arabidopsis embryos
Relations
SRA SRX037075
BioSample SAMN00189367

Supplementary file Size Download File type/resource
GSM595273_globular_WT_unique_read_count.txt.gz 331.6 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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