Get quote for 20 miRNA libraries

[sr320]

Manilla clam is species

[kubu4]

How much sequencing depth should we aim for? 20x? 10x?

[sr320]

20x

On Mon, May 20, 2024 at 10:45 AM kubu4 @.***> wrote:

How much sequencing depth should we aim for? 20x? 10x?

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[kubu4]

Azenta and Genohub quote requests submitted.

[sr320]

How about UW?

On Mon, May 20, 2024 at 11:08 AM kubu4 @.***> wrote:

Azenta and Genohub quote requests submitted.

— Reply to this email directly, view it on GitHub https://urldefense.com/v3/__https://github.com/RobertsLab/resources/issues/1902*issuecomment-2120948383__;Iw!!K-Hz7m0Vt54!ge9oJ08b11oh9ZVYKALI3spIyErYpUK_YMeiiQA6cTepbTwuy9CIVqBwwnZayLNVpOWMrYiojrmE-avX_24Czk4$, or unsubscribe https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/ABB4PNYZCNNEUBMUW5SHO7LZDI3ZLAVCNFSM6AAAAABH2QAXBKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMRQHE2DQMZYGM__;!!K-Hz7m0Vt54!ge9oJ08b11oh9ZVYKALI3spIyErYpUK_YMeiiQA6cTepbTwuy9CIVqBwwnZayLNVpOWMrYiojrmE-avX6950v-g$ . You are receiving this because you authored the thread.Message ID: @.***>

[kubu4]

Waiting on response to see if they can do sRNA-seq library construction.

[kubu4]

GenoHub quote: $4,100.00

A few things to note:

• I deferred to them on recommended sequencing parameters for sRNA-seq.
• 1 x 50bp reads
• 10M average reads/sample
• Using a Singular Genomics G4 sequencer (!?!)

Genohub_Quote_54151821_Confirmed.pdf

[kubu4]

UW has confirmed that they do not make sRNA-seq libraries.

[kubu4]

Azenta: $5,610

A few things to note:

• Using Azenta recommendations for sequencing.
• 2 x 150bp reads
• 20M average reads/sample

30-1035633055_R1.pdf

[sr320]

Let's go with azenta - @mgavery can you select samples?

[mgavery]

Yes, I can select samples. Is there someone who can meet me at the NWFSC with dry ice and I can hand them off? I'll be at the lab Tuesday and Thursday next week.

[kubu4]

I'll be in on Tuesday and can meet you.

[kubu4]

@mgavery - Change of plans for me. I won't be able to make it into tomorrow. Sorry about this!

Not sure if I'll be able to make it in on Thursday, either, but will update when I know more.

[kubu4]

Just following up to see the status on this. I'm guessing no one else coordinated with @mgavery to get samples?

If not, I'm planning on being in tomorrow and Thursday of this week. Please let me know if either of those work.

[mgavery]

Hi, Tuesday works for me. Any time after 10am.

[mgavery]

samples provided: 196,199,211,310,341,363,367,376,460,485 24,26,30,33,34,35,71,88,260,501

[kubu4]

@sr320 - Turns out these are tissue samples.

The quote I got was for total RNA.

Should I:

• Get updated quote, with tissue as starting material?

OR

• Plan on isolating RNA?

[kubu4]

Per discussion at Hack-a-thon today, will get updated quote for tissue as starting material.

[kubu4]

@mgavery - Which tissue are these?

[kubu4]

@mgavery - NM! I see it on the box (eggs).

[kubu4]

Updated Azenta quote:

$6,310 (~$315/sample)

30-1035633055_R2.pdf

@sr320 - Proceed with updated quote?

[sr320]

Proceed with updated quote?

yes

[sr320]

I added budget info in slack.