Information for DNR Revision

From email communication with Alex and Micah.


1. Time of day and height 2016 (from calendar and field notes):
Case inlet: T July 19 12:15 -1.8
Skok: Wed July 20 11:51 -1.8
Willapa: Th July 21 9:28 -1.7

I believe Port Gamble was T July 19 11:11 -1.6 and Fidalgo Bay was W July 20 12:12 -1.7′

2. The animals were pretty uniformly placed ~0.5m from the sensors at the same tide height. We had instruments in all habitat patches but did not get data from all of them.

3. Oysters were young of the year – probably ~2 months old.

4. I hate questions like that. I would answer along the lines of "it was beyond the scope of this paper" which is true since this paper is a lot about the development of the method and exploring protein results, ya? I would love to see an analysis combining the different things that we measured but that is complicated. For one, I don’t think we did protein and fatty acid on all of the same individuals. I remember adjusting the samples to try to do the same oysters but can’t remember how much overlap there was. If you would like, we could see if looking at growth or FA helps interpret some of the patterns you talk about in the current paper.


Collection dates for the first outplant (June to July 2016) and the second outplant (July to August 2016):

Round 1:
07.19.16: Oysters collected from Case Inlet at ~12:15pm
07.20.16: Oysters collected from Fidalgo Bay at ~12:15pm, and from Skokomish at ~12:00pm
07.21.16: Oysters collected from Port Gamble Bay at ~12:30pm, and from Willapa at ~9:15am

Round 2:
8.17.16: Oysters collected from Case Inlet at ~11:45am
8.18.16: Oysters collected from Fidalgo Bay at ~11:45am, and from Skokomish at ~11:30am
08.19.16: Oysters collected from Port Gamble Bay at ~12:00pm, and from Willapa Bay at ~8:45am

The timing of dissections varied a little, depending on how many people were there to help, but I believe that they were always completed within 3hrs of collection. Alex – I know you did some solo dissections at SK/WB. Do your field notes/memories reflect a 3hr window?

The tidal height at PG, SK, and WB was roughly -1ft MLLW; at CI & FB it was roughly -2.5ft MLLW.

The instruments and oysters were very close to each other (photo from PGE attached). The lateral distance was less than 1m, and the tidal height was the same for the animals and the instruments.

The oysters were 2-3months old at the time of outplant.

Regarding the reviewer comments, you could respond by circling back to the central goals and questions of the proteomics work. From the perspective of WDNR, we wanted to explore whether proteomics could provide a tool to diagnose stress in a species of high ecological and economic importance. If the techniques developed through this project were used as a diagnostic tool on animals collected from the field, we wouldn’t know the growth rate of that animal – we’d have expression patterns only. So to me, it actually makes sense to confine the manuscript to proteomics.

Kaitlyn’s notebook: Total protein abundances and unique proteins


I’m not sure how best to put this in a table. The third table is the best way I could think of right now. The first three tables are just to show differences between two silos only.


Grace’s Notebook: BLAST on Hummingbird and Transrate

Today I attempted to take my BLAST output on Hummingbird and work through this blast-2-slim notebook of Steven’s. I had gone through this before using Cgigas. I got stuck today at the part where you !join _blast-GO-unfolded.sorted with GO-GOslim.sorted. Will ask tomorrow. Additionally, today I worked on using transrate to look at my C. bairdi assembly using Laura’s notebook as a guide.

BLAST to GO slim

The notebook is in the Downloads on Hummingbird in grace-Cbairdi-transcriptome/notebooks/20181105-blast-Cbairdi_swiss-prot.ipynb. I couldn’t figure out how to commit and push it successfully to my GitHub repo notebook… but I rsync-ed the notebook to Owl from Hummingbird: /scaphapoda/grace/Crab-project/20181025-blast-Cbairdi_swiss-prot.ipynb.

Anyway, I got stuck where you have to !join the _blast-GO-unfolded.sortedwith GO-GOslim.sorted. I checked the two files in TextWrangler on Hummingbird, and they both looked good. Additionally, I looked at the files using !head and !tail. The one thing that I noticed, which I’m not sure is typical, is that in the _blast-GO-unfolded.sorted file, there were a lot more rows of the “TRINITY_DN#…” column, than there where of the “GO….” column. Maybe that is the problem?

Will ask Steven or Sam tomorrow morning.


I used Transrate today and followed Laura’s notebook. Here’s my notebook post: Cbairdi_01_tranrate.ipynb. I’m not sure what else I should do with this, so I’ll ask tomororw.


This Thursday is GSS. I’m hoping to have some basic assembly data to share on my poster, and I’ll have some stuff after I get the above issues sorted out.

from Grace’s Lab Notebook