|
| Status |
Public on Oct 30, 2017 |
| Title |
DAS454_T2s |
| Sample type |
SRA |
| |
|
| Source name |
developing green siliques
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: developing green siliques
transgene construct: DAS454
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
T2 seeds from pDAB454 transgenic plants
|
| 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 |
SAMN04439377 |
| SRA |
SRX1544138 |
