|
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 |