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Sample GSM838183 Query DataSets for GSM838183
Status Public on Nov 22, 2011
Title total amplified RNA, 2-to-4 cells Ler/Col embryos, sample # MC_LerCol_11
Sample type SRA
Source name embryos (dissected)
Organism Arabidopsis thaliana
Characteristics Stage: 2-to-4 cells embryo stage with suspensor (partial)
maternal strain: Landsberg erecta (Ler)
maternal genotype/variation: wildtype
paternal strain: Columbia_0 (Col0)
paternal 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.
Submission date Nov 22, 2011
Last update date May 15, 2019
Contact name Marc William Schmid
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
SRA SRX107220
BioSample SAMN00760311

Supplementary file Size Download File type/resource
GSM838183_MC_LerCol_11_unique_read_count.txt.gz 465.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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