Repository for data, analyses, code, and figures associated with the paper for Summer 2021 and Summer 2022 P. helianthoides Immune Response Sea Star Wasting Disease 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:
paper-pycno-sswd-2021-2022/data/RNAseq_library_metadata.csv
GitHub Repository back up (includes big files that can't be pushed to GitHub):
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.
Experiments A and B were performed, detailed below.
Personnel
Drew Harvell, Alyssa Gehman, Grace Crandall, Miranda Winningham, Paul Hershberger, Jake Gregg
Questions:
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 fresh for each experiment (note: 0.45um filtered only made for Experiment A):
Experiment A began on 9/23/2021. Stars were injected with either 0.45micron filtered live tissue homogenate from a wasting star (microbial group), heat-killed tissue homogenate from a wasting star (control group), or unfiltered live tissue homogenate from a wasting star (exposed group). Stars were observed 2x daily and sampled at disease sign along with control pair. The RNAseq data timeline control and exposed groups are not balanced due to lack of sufficient RNA for sequencing for some samples. Comparisons made for those libraries are shared below under the title “Experiment A”.
Experiment B began on 10/05/2021. Stars were injected with heat-killed tissue homogenate from a wasting star (control group) or unfiltered live tissue homogenate from a wasting star (exposed group). Some of the control stars in this experiment were previously injected with the 0.45micron filtered live tissue homogenate in Experiment A but never showed any disease signs, and so they became part of the control group. They continued to remain disease-sign free throughout the remainder of Experiment B. Comparisons made between libraries from Experiment B are shared below under the title “Experiment B”.