Marcel Keller (marcel.keller@ut.ee)
2022-01-26 14:00:47

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James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-01-26 14:01:43

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Gunnar Neumann (gunnar_neumann@eva.mpg.de)
2022-01-26 14:01:43

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ivelsko (velsko@shh.mpg.de)
2022-01-26 14:01:43

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Zandra Fagernäs (fagernaes@shh.mpg.de)
2022-01-26 14:01:43

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aidanva (aida.andrades@gmail.com)
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Maria Lopopolo (maria.lopopolo1989@gmail.com)
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Kelly Blevins (blevinske1@gmail.com)
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Marcel Keller (marcel.keller@ut.ee)
2022-01-26 14:07:22

question for protocols.io: it seems quite buggy, for example tables cannot be always edited after creation (right click menu to add rows etc.), but my most recent problem/question is: do all authors need to create profiles or can you also add them just as free text? If the latter should be the case I have discovered another bug.

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-01-26 14:08:03
  1. Yes, some parts of the interface can still be a bit buggy, but they are working on them.
  2. No, you can add as free text I believe
Marcel Keller (marcel.keller@ut.ee)
2022-01-26 14:08:57

okay then there’s another bug. it just shows the revolving loading icon instead of the “add” button

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-01-26 14:09:09
image.png
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-01-26 14:09:11

Works for me?

Marcel Keller (marcel.keller@ut.ee)
2022-01-26 14:09:34
Screenshot 2022-01-26 at 14.09.23.png
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-01-26 14:10:16
protocols-io2.gif
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-01-26 14:10:36

Maybe try refreshing the page, or adding a , at the end?

Katerina Guschanski (katerina.guschanski@ebc.uu.se)
2022-01-26 14:12:25

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Marcel Keller (marcel.keller@ut.ee)
2022-01-26 14:13:03

ah refreshing helped 🙈

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-01-26 14:13:12

Tha'ts normally my solutoin with protocols.io

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-01-26 14:13:19

Still better than anything I've used so far

Louis Lhote (louis.lhote@outlook.fr)
2022-01-26 14:14:23

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Marcel Keller (marcel.keller@ut.ee)
2022-01-26 14:15:00

A lot of manual work, but I’m getting there…

💪 James Fellows Yates
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-01-26 14:15:20

Yeah requires a bit of investment first time

Marcel Keller (marcel.keller@ut.ee)
2022-01-26 14:15:22

feels a bit like the beginning of pandora 😆

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-01-26 14:15:37

but every subsequent publication: fork, tweak that one step, YOUR HWOLE METHODS SECTION DONE

Marcel Keller (marcel.keller@ut.ee)
2022-01-26 14:16:41

yes, looking forward to that 👍

Zoé Pochon (zoe.pochon@gmail.com)
2022-01-26 14:37:56

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Zuzana Hofmanová (fajkosovaz@gmail.com)
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Biancamaria Bonucci (biancamaria.bonucci@ut.ee)
2023-02-23 10:15:19

Hi!!! I don’t know if this question falls better here or in <#C02DCKJ54JX|no-stupid-questions> but I guess it would be good for both channels aahha It is a lot that I have this question but I would like your thougths in this.. When you are dealing with dental calculus and you want to study oral microbiome, do you perform a decontamination before the extraction protocol? If yes, what do you use (EDTA wash, bleach and ethanol, some other buffer,..) and why? Why not? Have you tested different decontamination protocols and found statistically significative differences?

Thanks in advance ❤️

Katerina Guschanski (katerina.guschanski@ebc.uu.se)
2023-02-23 10:30:35

*Thread Reply:* We do UV surface decontamination and EDTA wash. Tested it on very few samples and not really systematically, but observed an increase in oral bacs after the treatment compared to before. Results for this are presented here: https://academic.oup.com/mbe/article/37/10/3003/5848415?login=false (check out Fig. S3 in Supp)

☝️ James Fellows Yates, Zandra Fagernäs
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-02-23 12:55:34

*Thread Reply:* Same for us too!

Tested by Andrew and Tina here: Ozga, A. T., Nieves-Colón, M. A., Honap, T. P., Sankaranarayanan, K., Hofman, C. A., Milner, G. R., Lewis, C. M., Jr, Stone, A. C., & Warinner, C. (2016). Successful enrichment and recovery of whole mitochondrial genomes from ancient human dental calculus. American Journal of Physical Anthropology, 160(2), 220–228. https://doi.org/10.1002/ajpa.22960

and our current protocol: https://dx.doi.org/10.17504/protocols.io.bqbmmsk6 (step 9 onwards)

protocols.io
Ancient DNA Extraction from Dental Calculus with Consolidant Removal
Silica-based total DNA extraction protocol optimised for the recovery of ultra-short DNA molecules from archaeological dental calculus, modified from Dabney et al. (2013) PNAS (...
Original URL: https://dx.doi.org/10.17504/protocols.io.bqbmmsk6
Sterling Wright (sterlingwright2016@utexas.edu)
2023-02-23 15:17:47

*Thread Reply:* You may be interested in this paper: https://www.nature.com/articles/s41598-021-86100-w

We explored how the commonly used decontamination methods impacted the recovery of oral microbes. It doesn’t seem like to be a huge difference among a couple.

Nature
Effectiveness of decontamination protocols when analyzing ancient DNA preserved in dental calculus
Scientific Reports - Effectiveness of decontamination protocols when analyzing ancient DNA preserved in dental calculus
Original URL: https://www.nature.com/articles/s41598-021-86100-w
👍 James Fellows Yates, Biancamaria Bonucci
Biancamaria Bonucci (biancamaria.bonucci@ut.ee)
2023-02-23 16:31:45

*Thread Reply:* Thank you so much everyone!
☺️

👍 Sterling Wright
Marcel Keller (marcel.keller@ut.ee)
2023-09-07 14:46:23

A question for those working with the Santa Cruz Protocol: am I right to assume that this protocol is compatible with the “NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs)” sets (e.g. NEB E6440S) for indexing?

Joshua Kapp (jkapp@ucsc.edu)
2023-09-07 15:45:18

*Thread Reply:* Correct, the NEB indexing primers are compatible with the SCR.

🙏 Marcel Keller
Katerina Guschanski (katerina.guschanski@ebc.uu.se)
2023-11-14 20:13:11

Hi community, we are thinking of scaling up our wet lab protocols for ancient dental calculus to allow processing more samples at once. We are currently doing everything manually (extractions, library preps, clean-up), sample by sample, not even using a manifold. What are peoples' approaches and kit for multi-sample processing? I think the development has passed me by, so would be happy to hear the best hacks (except that robots are definitely outside of our budget!)