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| Status |
Public on Jul 07, 2018 |
| Title |
Small RNA (sRNA) sequencing data from pre-meiotic and meiotic anthers of Asparagus |
| Organism |
Asparagus officinalis |
| Experiment type |
Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
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| Summary |
Purpose: To study pre-meiotic (21-nt) and meiotic (24-nt) phasiRNA pathways in non-grass monocots
Methods: Anthers were dissected using a 2 mm stage micrometer in a stereo microscope, and immediately frozen in liquid nitrogen until total RNA isolation was performed. Small RNA, mRNA libraries were generated using short-read (Illumina) and Single Molecule Real Time SMRT (PacBio) sequencing approaches. Stages were assigned based on the morphology of archesporial (AR) and tapetal cells of A. officinalis (Asparagus) anthers.
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| Overall design |
Flowering Asparagus plants were harvested from T.S. Smith and Sons Farms (Bridgeville, Delaware). Buds corresponding to pre-meiotic and meiotic stages were used to generate mRNA, full-length and sRNA libraries. Data from mRNA-seq and SMRT-seq were used for de novo transcriptome assemblies. These assemblies were then used along with sRNA data to identify phased-siRNA precursor transcripts and other protein factors that play a role in reproductive phasiRNA pathways. mRNA-seq assembly was performed using “Trinity RNA-Seq assembler”, full-length transcript assembly was prepared using “SMRT-tools” (v2.3) provided by Pacific Biosciences. Phased siRNA precursors were identified using “PHASIS suite” (https://github.com/atulkakrana/PHASIS/wiki), and transcripts sfor protein-coding genes were identified using “Trinotate” (https://trinotate.github.io/).
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| Contributor(s) |
Kakrana A, Mathioni S, Shevchenko O, Kingham B, Meyers BC |
| Citation(s) |
30002159 |
| |
| Submission date |
Apr 06, 2018 |
| Last update date |
Jul 23, 2018 |
| 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 |
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| Platforms (2) |
| GPL24857 |
Illumina HiSeq 2500 (Asparagus officinalis) |
| GPL24858 |
PacBio RS II (Asparagus officinalis) |
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| Samples (37)
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| Relations |
| BioProject |
PRJNA449052 |
| SRA |
SRP137811 |
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