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Sample GSM1986905 Query DataSets for GSM1986905
Status Public on Oct 30, 2017
Title DAS588_018s
Sample type SRA
 
Source name developing green siliques
Organism Arabidopsis thaliana
Characteristics tissue: developing green siliques
transgene construct: DAS588
copy number of transgene: single copy
multigene construct design: canola-biased coding sequences for PFA1, PFA2, PFA3, and HetI genes
Extracted molecule total RNA
Extraction protocol Materials were collected and flash frozen in liquid nitrogen. Total RNA was extracted by method described in BMC Research Notes 1, p.93-9 (2008). Genomic DNA was extracted by method described in Nucl. Acids Res. 8, p.4321-25 (1980).
Small RNA libraries were constructed using Illumina Truseq small RNA sample preparation kit (RS-200-0012). RNAseq libraries were constructed using Illumina Truseq RNA library Preparation kit v2 (RS-122-2001). Methyl C-seq libraries were constructed using method described in Nat. Prot. 10, 475-83 (2015).
 
Library strategy ncRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina HiSeq 2000
 
Description small RNA
T4 seeds from pDAB588 transgenic plants, "event.plant": 042.018
Data processing For data processing, the adapter sequences were trimmed from raw sequence reads. The small RNA sequences were further trimmed to the lengths between 18 and 34 nucleotides. RNA-seq sequences were maintained at the length after adapter trimming.
Sequence data processing was conducted using in-house Perl scripts developed by Meyers lab in University of Delaware
Genome_build: AT_TAIR10_genome
Supplementary_files_format_and_content: tag count file
 
Submission date Dec 29, 2015
Last update date May 15, 2019
Contact name Blake C. Meyers
E-mail(s) bmeyers@danforthcenter.org
Phone 314-587-1422
Organization name Donald Danforth Plant Science Center
Lab Meyers lab
Street address 975 N Warson Road
City St. Louis
State/province MO
ZIP/Postal code 63132
Country USA
 
Platform ID GPL13222
Series (2)
GSE76406 GC-rich coding sequences reduce transposon-like sRNA-mediated transgene silencing in Arabidopsis and maize
GSE103112 GC-rich coding sequences reduce transposon-like sRNA-mediated transgene silencing in Arabidopsis and maize
Relations
BioSample SAMN04439370
SRA SRX1544158

Supplementary file Size Download File type/resource
GSM1986905_DAS588_018s_chopped.txt.gz 22.2 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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