Develop 2 month plan process Hawaii Oyster Samples

[sr320]

Regarding ploidy and epigenetics

[sr320]

bulk of the samples we have from Hawaii

https://robertslab.github.io/sams-notebook/2019/12/10/Samples-Received-Pacific-Oyster-Tissues-from-Hawaii-(Maria-Haws)-from-High-and-Low-pCO2.html

[sr320]

Is there a data sheet associated with samples Ronit worked with?

[sr320]

lets do some deep triploid v diploid comparisons

[kubu4]

Link to Ronit's ploidy sample sheet:

https://docs.google.com/spreadsheets/d/e/2PACX-1vTHPB2YUKnaZ_-OKJR2fWATWSlcDFADULn_1pjz1_2BYh9gSpRW-VHKwpdCFmlvxfiR1C8g7DsAoxHx/pubhtml?gid=0&single=true

[kubu4]

Also have triploid C.gigas (n = 4) from Nisbet Oyster Co. Collected ctenidia, gonad, mantle, muscle from each.

https://robertslab.github.io/sams-notebook/2018/02/28/samples-received-triploid-crassostrea-gigas-from-nisbet-oyster-company.html

[sr320]

@kubu4 what would be the cost for 10 samples RNA-seq and when would they have to be submitted to be billed by end of August?

Same for Bisulfite Seq (presuming WGBS which would require deeper coverage)?

[kubu4]

Does it matter where we submit?

[kubu4]

Sorry, I should have phrased it: Can we submit them anywhere?

[kubu4]

Also, what type of sequencing depth are we looking at for the BSseq?

[sr320]

Anywhere is fine, maybe run a couple of options, one being UW.

On Jul 1, 2020, 6:00 AM -0700, kubu4 notifications@github.com, wrote:

Sorry, I should have phrased it: Can we submit them anywhere? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

[sr320]

Not quite sure, - can see if what recommendation might be. Wild guess is 100x

Also worth getting idea if we did do MBD-BS (less coverage) with 20x probably sufficing.

Yaamini’s recent paper can provide good estimate for MBD-BS coverage

On Jul 1, 2020, 6:06 AM -0700, kubu4 notifications@github.com, wrote:

Also, what type of sequencing depth are we looking at for the BSseq? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

[kubu4]

Genewiz quotes (guaranteed <20 business days). Outputs listed below are based on Genewiz's recommendation based on genome size.

RNAseq (20 - 30M reads; 150bp PE; stranded):

• $4100

---

WGBS (>30x coverage; 150bp PE):

• $8390

---

EDITED: Added note about Genewiz recs.

[kubu4]

NWGC (UW) can bill by the end of August if we submit samples no later than July 20, 2020.

RNAseq (~30M reads):

• $2599.45

[kubu4]

Now, just waiting on ZymoResearch. Should have a call today with a project manager.

[kubu4]

ZymoResearch quotes:

RNAseq (30M reads; 150bp PE; stranded):

• $3250

Waiting on them to update WGBS quote, due an oversight on their end.

[kubu4]

ZymoResearch quote:

WGBS (>30x coverage; 150bp PE):

• $11,000

[kubu4]

I should add that I think that Zymo WGBS quote is calculated incorrectly (I think it is for far greater than 30x coverage). I've sent a message to them to double-check the math.

[kubu4]

Alrighty, updated quote from Zymo:

WGBS (>30x coverage; 150bp PE):

• $5,000