Get RNA-seq quote (coral)

[sr320]

Corals for 116 stranded RNA-seq libraries

Sending RNA

20M reads

[sr320]

Would hope we could get this number with Azenta https://d.pr/i/SzaMHH

[kubu4]

Can you please share link for promo? I can't seem to find that.

[sr320]

https://web.azenta.com/promotions?utm_medium=email&_hsenc=p2ANqtz-8nQwvqLYT_f2vLkTUwnFcWiFYEtmNUL-9YxEznRwEYqtbkL_0YoyBqMCSO2q1gIWwxMtF1Mtzyn5Bx7APBTIjAp5sOhA&_hsmi=310339430&utm_content=310319944&utm_source=hs_email

[kubu4]

Quote request, with promo code, submitted.

[kubu4]

:crossed_fingers:

Just saw in the fine print that this pricing is limited to new academic customers...

[kubu4]

Azenta:

Looks like they applied a different promotion (15% off RNA-seq). Here's the quote:

$17,433.50 (~ $150/sample)

30-1047560508_R2.pdf

[kubu4]

Have requested quote from UW NWGC.

[sr320]

@kubu4 anything back from UW?

[kubu4]

Nope. Sent a follow up email.

[kubu4]

UW quote: $27,105.95

~ $235/sample 2024-06_017.pdf

[sr320]

lets move ahead with Azenta quote - getting PO etc

[kubu4]

PO request initiated.

[kubu4]

Have the PO number.

Need the following sample submission form filled out:

30-1047560508_NGS_Template_File.xls

[sr320]

PO number?

[kubu4]

PO-0100084783

[sr320]

thanks!

[sr320]

@kubu4 can you get a modified quote where they do RNA-seq AND miRNA (short RNA) seq on same RNA sample? (116 samples)

[kubu4]

sRNA-seq quote (using same set of input RNA): $32,110

30-1069297013.pdf

To make sure this is clear, this is in addition to the previous RNA-seq quote.

[sr320]

can you get PO for this (or will the same PO work?)

[kubu4]

PO request for sRNA-seq submitted.

[kubu4]

PO for sRNA-seq: PO-0100091376

[kubu4]

Sample sheet needs to be filled out:

30-1069297013_NGS_Template_File.xls

[sr320]

update to 120 samples

[kubu4]

Updated sample counts submitted earlier. Will report when updates are received.

[kubu4]

Updated sRNA-seq quote:

$33,210.00

30-1069297013_R1.pdf

Sample sheet needs to be filled out:

30-1069297013_NGS_Template_File.xls

[kubu4]

Updated RNA-seq quote:

$18,028.50

30-1047560508_R4.pdf

Sample sheet needs to be filled out:

30-1047560508_NGS_Template_File.xls

[JillAshey]

Perfect! I'll start pulling samples today!

[JillAshey]

e5_sequencing_samples.xlsx - azenta_rna.csv Sample sheet for Azenta RNA submission

[kubu4]

@JillAshey - I'm unable to upload the sample sheet you've provided above - the system throws an error.

I'm guessing it's because you've added columns.

Please be sure to keep the form exactly as provided by Azenta. Additionally, please keep it in Excel format.

Thanks and sorry for the hassle.

[zdellaert]

Hi all, I was preparing our list to aliquot the RNA into plates tomorrow to send to Azenta on Monday, and realized that I've already sent 6 of these tubes to Azenta for the deep dive in April 2023 for both RNA seq and small RNA (30-789513166 and 30-852430235_R3) . So, 1) we've already sequenced them and 2) we don't have those tubes in the freezer anymore. Do we need to ask for an updated quote for fewer samples?

[zdellaert]

Unless we run into any missing samples tomorrow, this should be the final list for Azenta:

Azenta_E5_RNA_Sequencing.xlsx

[AHuffmyer]

Can you direct me to the list of those that were sent previously? We need to make sure to avoid batch effects do not confound time/site/species effects.

All samples should have another molecular sample in the freezer that has not yet been extracted. The original extractions were done on one of two molecular tubes with biopsies. I suggest we re extract these samples from the second molecular replicate to send for sequencing. Thoughts?

[zdellaert]

See tab WHOLE SAMPLE SENT TO AZENTA -- RNA Aliquot April 5;

https://docs.google.com/spreadsheets/d/1r3oGvGsLLe9fI9mktjg0MM5yMIUpUnTeiNV45gZvLFs/edit?usp=sharing

30-789513166_NGS_SampleInfo_File_HP.xls

They were sent on April 5, 2023 and the whole volume was split for stranded RNA seq and small RNA seq

37926916-62e5-4076-8fc3-68c32c61b791.pdf 402832dd-6a98-4a9f-b318-a08f1ab0e5fd.pdf

[zdellaert]

Hi all,

Just got off the phone with Ariana, who has concerns about the batch effect of having these 6 samples sequenced in a previous run, especially since they were all from the same timepoint (TP2) and site 1. The colonies are: POC-53, POC-57, POR-73, ACR-145, ACR-150, and ACR-173.

@sr320 and Hollie, we wanted your thoughts on this batch effect issue and whether we should:

1) Re-extract RNA from these samples, possibly delaying the RNA shipment by a few days if any issues arise (if there is material left and RNA is good on extraction we could still likely get RNA shipped on Monday)

or

2) Send the 111 samples we already have extracted and use the previous deep dive data for the 6 samples already sequenced. Ariana is worried this will cause difficulty to parse out site/timepoint differences if there is a strong sequencing batch effect given that all the deep dive samples were from one site and timepoint.

[sr320]

New extractions

[zdellaert]

Plates are done and in the freezer, ready to be shipped out on Monday. Final sample sheet for Azenta attached. 20240816_Azenta_E5_RNA_Sequencing.xlsx

[AHuffmyer]

Were you able to perform new extractions using existing tissue in molecular shield tubes?

[JillAshey]

Yes that info is here: https://github.com/JillAshey/JillAshey_Putnam_Lab_Notebook/blob/master/_posts/2024-08-16-MiniprepPlus-DNA%3ARNA-extractions-E5.md

[JillAshey]

Tracking number for RNAseq package: 778050045280. Will be picked up today and delivered tomorrow morning