Get Seq Quote - coral samples

[sr320]

18 samples - have total RNA need RNA-seq and sRNA libraries (to look at miRNA expression). Looking for about 40-50 M reads 100PE.

thinking UW and Azenta?

[sr320]

Azenta seems to have some promos https://web.azenta.com/promotions

[kubu4]

How was total RNA isolated?

Reason: E.g. RNAzol has different protocols depending on whether or not one wants to include sRNAs...

[kubu4]

Also, what're genus/species (needed for Azenta quote)?

[sr320]

@hputnam - info on RNA extraction?

species = montipora capitata

[hputnam]

species = Acropora pulchra

Extraction = https://www.zymoresearch.com/products/quick-dna-rna-miniprep-plus-kit

[kubu4]

Azenta:

smallRNA-Seq: $8,120 RNA-Seq: $4,240

UW does not do smallRNA-Seq.

Will get quote for regular RNA-Seq.

[kubu4]

UW RNAseq quote: $3528.38

[sarahtanja]

^Is your UW quote from PacBio Sequencing Service or Northwest Genomics Center?

[kubu4]

Neither. It's from Azenta.

[sarahtanja]

Thank you! I'm looking for similar quotes for a separate project and was snooping here.

[kubu4]

Gah! Sorry! Just realized there were mutliple quotes in this Issue.

You probably were referring to the one you pointed to :

^Is your UW quote from PacBio Sequencing Service or Northwest Genomics Center?

Sorry about that. Was on mobile when I responded.

Anyway, it's from Northwest Genomics Center.

Earlier in the Issue, the quotes are from Azenta.

[sr320]

@kubu4 ok - almost ready to send but now need quote for 15 instead of 18.. Only looking at RNA--seq now. https://web.azenta.com/promotions ?

[kubu4]

Update UW quote:

• $3560.84

[sr320]

thats crazy - you would think with time cost would go down, not up :) (it was cheaper to do more samples in December)

[kubu4]

Yeah, they addressed this in their reply:

Hi Sam,

Attached is a new quote for 15 samples instead of 18. Since the original quote was written, our Center had new rates go into effect, and all of the Illumina reagents had a price increase. These changes are reflected in the attached quote.

[kubu4]

Aaand, just got updated Azenta quote:

• $3349.50

[sr320]

Will go with Azenta - @hputnam will be sending 15 RNA to Azenta. what info does she need, a quote #?

[kubu4]

I'll need to get a PO first. Which budget(s) should I use?

[sr320]

dropped in slack

[kubu4]

While I get PO set up, @hputnam, please download and fill out the attached sample submission form (Excel). Please email back to me when it's completed and I'll let you know when Azenta is ready for the samples. Thanks!

• Sample submission form: 30-789513166_NGS_Template_File.xls

Also, here are the sample guidelines:

Follow these guidelines when preparing and submitting your samples. Sample Type: Total RNA

Recommended Amount: >2 µg @ >50 ng/µL

Minimum Amount: 500 ng

Purity (A260/280): 1.8-2.2

Recommended RIN: ≥6.0

Buffer: Nuclease-free water

Tubes/Plates: For projects with <36 samples, prepare samples in clearly labeled microcentrifuge tubes. For larger projects, use 96-well PCR plates.

Shipment Method: Dry ice or RNA Stabilization Tubes (see below)

[sr320]

update: @hputnam predicts the can get done early next week

[sr320]

@kubu4 can you get a quote for miRNA on same samples.... based on Javi E5 conversations... maybe https://www.realseqbiosciences.com ; or genohub

[kubu4]

Quote for miRNA sequencing (2x50bp) of 15 total RNA samples via Genohub:

• $6,963.16

[hputnam]

@kubu4 here is the sample submission sheet for Azenta 30-789513166_NGS_SampleInfo_File_HP.xls

[hputnam]

30-818144933_R2.pdf

This is what I have for another coral project from Azenta with $369 per sample and the Genohub was $464. @kubu4 can you request 15 sample quote from Azenta through their portal?

[kubu4]

an you request 15 sample quote from Azenta through their portal?

I'll need more info.

How many reads per sample?

Paired-end or single-end?

Stranded or unstranded?

Species?

here is the sample submission sheet for Azenta

Thanks! I'll get this submitted sometime today and send you shipping info. Plan on sending samples next week, once I've let you know that the order has been submitted and is ready.

[hputnam]

@kubu4 we can match the specs of the quote I added that above for Azenta. Illumina, 2x150bp, ~350M PE reads (~105GB), single index. It is the same species and sample IDs as the file for the mRNA

[sr320]

Use what is in quote she provided for deets - species = Acropora pulchra

[kubu4]

@hputnam

Here's the quote I received from Azenta for that A.poculata sRNA sequencing: $9,114.00

Looks like the primary difference is that the quote I received is using two lanes of sequencing... Weird.

• 30-852430235.pdf

[sr320]

@kubu4 sorry we this quote for 15 samples not 20.... Same sample sheet as for RNA-seq

[kubu4]

Ah! Gotcha. Thanks for clarifying. BRB...

[kubu4]

Sorry about the confusion!

Updated quote for 15 samples: $5922.00

Quote:

• 30-852430235_R3.pdf

[sr320]

@kubu4 thanks - @hputnam green lit this - so you can move forward with. Which I presume is get PO etc. Just let @hputnam when she can send samples.

[kubu4]

Same budget as the previous set of samples?

[sr320]

Yes please

[kubu4]

@hputnam - Order for 30-852430235_R3.pdf (15 coral sRNA-seq) has been submitted.

Please print and include these forms with the shipment:

• 402832dd-6a98-4a9f-b318-a08f1ab0e5fd.pdf

Please ship samples to same address as previous order.

BTW, if these are actually the same exact samples as the previous order (i.e. a single tube of RNA that is to be split between the two projects), I'd recommend contacting Azenta to explain this.