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| Name | Last modified | Size | Description |
|---|---|---|---|---|
| Parent Directory | - | ||
| analyses/ | 2024-06-01 14:11 | - | |
| code/ | 2024-06-03 09:11 | - | |
| data/ | 2024-06-06 09:42 | - | |
| blastdb/ | 2024-06-25 14:27 | - | |
| paper-pycno-sswd-202..> | 2024-11-04 19:19 | 205 | |
Repository for data, analyses, code, and figures associated with the paper for Summer 2021 and Summer 2022 P. helianthoides Immune Response SSWD work.
P. helianthoides genome: https://www.ncbi.nlm.nih.gov/datasets/taxonomy/7614/
P. helianthoides genome annotation files: https://datadryad.org/stash/dataset/doi:10.5061/dryad.51c59zwfd
Summer 2021 trimmed RNAseq reads (Raven):
/home/shared/8TB_HDD_02/graceac9/data/pycno2021
Summer 2022 trimmed RNAseq reads (Raven):
/home/shared/8TB_HDD_02/graceac9/data/pycno2022
RNAseq library metadata:
In the summer of 2021, adult Pycnopodia helianthoides were collected (Permit: Harvell 21-1172) by a team of WDFW divers and brought to USGS Marrowstone Field Station.
Stars were observed for several weeks and any that showed signs of disease were not used for experiments.
Several experiments were performed, but I have RNAseq data from Experiment 2 - details below.
Questions:
1. Is Sea Star Wasting Disease transmissible? 2. If yes, is the
causative agent in the small size fraction?
Multiple tissue types from an adult Pycnopodia helianthoides wasting from the field were blended together using a Tissue Tearor (link; Tissue Tearor 985370-07 Homogenizer; 120 VAC, 1.2 A). The sample was then spun down to pellet larger bits of tissue. The supernatant was then used as the inoculum for experiments.
The following inoculate types were made:
1. Heat-killed (control): supernatant was placed in a falcon tube and
held in boiling water with a stir bar for 10 minutes 2. 0.45um filtered
(exposed): supernatant was filtered through a vacuum bottle unit -
flow-through is larger viruses and bacteria 3. unfiltered (exposed):
supernatant was unfiltered, so it would contain anything from a large
protist to a small virus
Due to this summer being in the very early stages of our group’s work, aspects of this work was a bit more on the exploratory side and there were several different inoculation dates.