RobertsLab
Get Quote for coral WGBS
Quotes have been requested from Azenta, Zymo, and GenoHub.
BTW - quotes are based off of 20X coverage for 500Mbp genome size.
EDITED: Added info about coverage and genome size.
Genohub quotes are in.
23,664.00
Genohub_Quote_55027585_Confirmed.pdf
$27,003.47
Genohub_Quote_55011817_Confirmed.pdf
Apparently Zymo saw our quote request come across Genohub and they realized their initial quote was "wrong." Here's the updated quote.
$31,911.60
Quote_QUO18419_1722971332835.pdf
@sr320 @kubu4 Confirming Steven's preference for Azenta. I will have Jill and Zoe move forward with DNA aliquots for Azenta 30-1067895835_R2.pdf
Have requested updated quote for 120 samples. Will post sample sheet submission form when I received revised quote.
Updated quote:
$28830.00
Sample sheet needs to be filled out:
30-1067895835_NGS_Template_File.xls
Will request PO number.
Azenta requires 500ng of DNA for WGBS. Looking over the DNA concentrations, we have ~34 samples that have less than that. I'm not sure if we should send samples with <500ng. We should decide if we need to re-extract these. Either way, we likely have to push back sending the DNA samples out.
Today, Zoe and I can either re-extract the 34 DNA samples or prep the RNA plates.
From Azenta: Thanks for your interest in Genewiz Multiomics Solutions! Our methylation sequencing workflow kit says it will work well with inputs as low as 10 ng of DNA. However, our lab prefers to have at least ~300ng of input DNA given our internal workflow optimizations.
I told them that we have a quote for 120 samples and that 37 of those samples have <500ng and 12 samples have <100ng. Zoe and I were thinking about re-extracting/pooling some of the samples.
When I told Azenta this info, they said: For samples under 200ng or so, we can proceed at best-efforts. Like I said, we have a lot of experience working with less-than-optimal samples and often see good results with starting materials as low as 10ng. However, if you were able to re-extract and/or pool samples to have more starting material, that would be a good option.
@sr320 based on Jill's chat with Azenta and thinking about potential batch effects, Jill and I discussed and propose the following for your approval.
The samples are in RNA/DNA shield, which has lysed the cells and made the liquid a homogenized nucleic acid pool so the RNA and DNA have the potential to be directly related. Due to this I can't think of super strong effects from doing another extraction of DNA and adding the DNA to the previously extracted DNA to bring all of the total ng to the same amount to submit to Azenta. This way all of the library preps and sequencing would occur at the same time. We can then also after the sequencing examine statically for any extraction batch effects. @sr320, do you agree with this approach? If so, Jill will move ahead for the necessary re-extractions, aliquoting, and shipment to Azenta based on the PO number from Sam above.
Sounds like a good plan to me....
(as a side note can we get metabolomic test samples out prior to re-extraction if not already sent out?)
Thanks @sr320 ! @JillAshey can you switch the priority order to metabolomic test samples then DNA re-extraction? Thanks @JillAshey !