|
| Status |
Public on Aug 05, 2014 |
| Title |
S_delta35S |
| Sample type |
SRA |
| |
|
| Source name |
mix-stage inflorescence_S_delta35S
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
developmental stage: mixed-stage
tissue: inflorescence (contain majority of unopened flower buds)
genotype/variation: mutant defected in RNA polymerase II-transcribed trigger for generating silencing siRNA for RdDM, without the Target (T) locus
|
| Treatment protocol |
N/A
|
| Growth protocol |
N/A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mix-stage inflorescence (contain majority of unopened flower buds) were collected and flash frozen in liquid nitrogen. Total RNA was extracted by Tri reagent (Molecular Research Center, Inc.) according to manufacturer's protocol.
Small RNA libraries were constructed from 1 microgram of total RNA using Illumina Truseq small RNA sample preparation kit (RS-200-0012).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
sRNA-seq
Genome-wide small RNA profiling
segregate plants from cis mutant TS_delta35S, contains silencer (S) locus with deleted 35S promoter but no T locus
|
| Data processing |
For data processing, the adapter sequences were trimmed from raw sequence reads, and then the small RNA sequences were trimmed to the lengths between 18 and 34 nucleotides.
Sequence data processing was conducted using in-house Perl scripts developed by Meyers lab in University of Delaware
Genome_build: TAIR10
Supplementary_files_format_and_content: Tag count (.txt) file
|
| |
|
| Submission date |
Jun 11, 2013 |
| 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 (1) |
| GSE47852 |
Structural Variant of a Tandem Repeat-containing Silencer Locus Reveals Distinct Pol II and Pol IV-dependent Pathways of siRNA Biogenesis |
|
| Relations |
| BioSample |
SAMN02199183 |
| SRA |
SRX301584 |
