Hodgkins2023 #1117

DianaSpurite · 2023-09-28T12:39:47Z

Adding Hodgkind2023 samples

Pull Request

This PR is for a

New Publication(s)
Correction

For the following list(s):

ancientmetagenome-environmental (README)
ancientmetagenome-hostassociated (README)
ancientsinglegenome-hostassociated (README)

New Publication

Publication Information

This pull request is to add samples from the following publication(s):

This is to close #1109

Checklist

Publication is published (preprints currently not accepted)?
Checked the publication is not already in the database?
Checked samples in this publication are not previously published data (newly re-sequenced metagenomes are OK!)?
Samples are shotgun metagenomes (hostassociated-singlegenome may also contain whole-genome enriched data)?
Checked the list follows conventions as described in the corresponding sample type's README file (e.g. using ERS/SRS accession codes for ENA/SRA)?
Changelog is updated to include the publication under 'Added'?
Pull request has passed validation checks (see automated comment from github-bot)?
Review requested from @SPAAM-community/ancientmetagenomedir?
(If applicable) Made a separate PR to add new categories to controlled lists (stored under /assets/enums, e.g. material or archive)? If so the corresponding PR is here: Hodkins2023 singlegenome_species.json #1118

Adding Caruana2023 samples

Adding Caruana2023 libraries

added Caruana 2023

Correcting library_Polymerase

DianaSpurite · 2023-09-28T13:04:18Z

I'll leave a bunch of comments with information later today to help with reviewing process

Adding the correct name of the author

- added the correct author's name - corrected the last polymerase - added under-strokes in the library names for Deir-Rifeh-KNIII-Tooth and Deir-Rifeh-KNII-Tooth sample libraries

replaced the wrong author with the correct one - Hodgkins2023

DianaSpurite · 2023-09-28T18:33:02Z

When the species PR is approved the commit should become validated

DianaSpurite · 2023-09-28T18:46:49Z

For the reviewer(s):

SAMPLES:

All sample information is taken from Hodgkins 2023 publication supplementary table and main text, including sample age, sample material and coordinates (shortened in some cases to 3 decimals). Excluding PRJ numbers, SRS/ERS numbers and subsequently which archive.
Tenerife-004-Tooth sample age not provided, therefore I set it the same as the age of the other sample from the same site
For Vác-Mummy-Tissue sample, the material was stated to be "left chest extract", so I set it as simply "tissue"
Pericues-BC28-Bone sample age left as 550 as I wasn't sure if I should round up or down

DianaSpurite · 2023-09-28T19:44:19Z

For the reviewer(s):

LIBRARIES:

Links to all the original studies for each sample are available in the Hodgkins supplementary table "Supp Data 2"

I looked for the information here:

Sanganji-A1-Tooth and Sanganji-A2-Tooth: https://pubmed.ncbi.nlm.nih.gov/27581845/ -> ENA -> supplementary information -> Listed protocol
Deir-Rifeh-KNIII-Tooth and Deir-Rifeh-KNII-Tooth: https://doi.org/10.1016/j.jasrep.2017.12.025 -> ENA -> main text -> Listed protocol (Meyer and Kircher, 2010)
Augsburg-Tooth -> our records sample: "1343UnTal85"
Tenerife-011-Tooth; Tenerife-004-Tooth; GranCanaria-005-Tooth; GranCanaria-008-Tooth; Tenerife-012-Tooth; Tenerife-013-Tooth: https://pubmed.ncbi.nlm.nih.gov/29107554/ -> main text -> ENA
Tepos_35-Tooth: https://pubmed.ncbi.nlm.nih.gov/29335577/ unfortunately I didn't note this one for some reason..
Cueva_de_los_Lagos-Tooth: https://pubmed.ncbi.nlm.nih.gov/29531053/ -> main text -> ENA -> Kircher et.al protocol, age for this sample middle from the listed "late Bronze Age"
Yámana-Tooth: https: //pubmed.ncbi.nlm.nih.gov/29632188/ -> ENA -> suplement table
Vác-Mummy-Tissue: our records, sample "92-A1"
Chinchorro-Mummy-Bone and Pericues-BC28-Bone: https://pubmed.ncbi.nlm.nih.gov/26198033/ -> ENA -> supplementary information
Marseille-Tooth -> our records, sample "OBS107"
Barcelona-3031-Tooth -> our records, sample "Barcelona3031"
SLC-France-Tooth: https://pubmed.ncbi.nlm.nih.gov/30478041/ -> didn't note, unfortunately
Karolva-Tooth: https://pubmed.ncbi.nlm.nih.gov/31594508/ ->ENA -> supplementary information
Abusir1655-Tooth; Abusir1595-Tooth; Abusir1668-Tooth; Abusir1671-Tooth; Abusir1607-Tooth: https://pubmed.ncbi.nlm.nih.gov/32859198/ -> ENA -> main text -> listed protocols
Dacaozi-Tooth: https://pubmed.ncbi.nlm.nih.gov/32483115/ -> ENA -> main text -> listed protocols (36, 37)
Riga_Cemetery-Tooth -> our recoreds, sample "G701"
Chincha-UC12-12-Tooth; Chincha-UC12-24-Tooth; Chincha-UC8-8168-Tooth: https://pubmed.ncbi.nlm.nih.gov/32661160/ -> ENA -> main text -> protocol ref. 71 -> in that protocol ref. 2 & 3, not sure about polymerase for this sample
Chiribaya_Alta-Bone and El_Yaral-Bone-> our records samples "sample 54" and "sample 64", however, library treatment appeared to mismatch in our records and the Hodgkins 2023 supplement table. Main text in the original publication didn't state anything about treatment: https://pubmed.ncbi.nlm.nih.gov/25141181/
Peru-NA40-Bone; Peru-NA42-Bone: https://pubmed.ncbi.nlm.nih.gov/24568772/ -> ENA -> main text -> listed protocol (KAPA)
Pueblo_Bonito-Tooth: https://pubmed.ncbi.nlm.nih.gov/28221340/ -> ENA, layout listed as paired, but appears to be single is 3 of the libraries
Gniezno-Tooth: https://pubmed.ncbi.nlm.nih.gov/28609785/ -> ENA -> protocol Meyer and Kircher. ref. 73, I listed "single stranded" but was confused about it
Punta_Candelero-Tooth: https://pubmed.ncbi.nlm.nih.gov/31710665/ -> ENA -> protocol Meyer and Kircher, fastq assumed for this sample
Sample age and library treatment from Hodgkins 2023 UNLESS info comes from "our records".
Our records simply copied everything from archive information to download sizes.

correcting author

github-actions · 2023-09-28T19:49:09Z

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_samples.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_samples.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_samples.tsv is valid

Libraries

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_libraries.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_libraries.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

DianaSpurite · 2023-09-29T07:36:41Z

Sample age calculated considering 1950 as the present time

iseultj · 2023-09-29T14:57:07Z

Hi Diana, Thanks for doing this! I noticed a couple of things:

For Sanganji-A1-Tooth and Sanganji-A2-Tooth, it says the polymerase is unknown- I checked the Qiagen multiplex PCR handbook, and it looks like they use a HotStarTaq polymerase, but I'm not sure if that's what they actually used.

For Deir-Rifeh-KNIII-Tooth and Deir-Rifeh-KNII-Tooth - you put half-udg but I can't find any reference to it in the original paper?

For Tepos, I think the polymerases used were Accuprime (Taq) polymerase and then further amplification with Herculase II Fusion DNA Polymerase (agilent)

For the Chincha samples, it might be best to leave the polymerase as unknown? I wasn't able to figure it out either....

For Chiribaya_Alta-Bone and El_Yaral-Bone-in the supplement, it does state it's UDG treated, so I think ok to leave as is.

Finally, for Pueblo_Bonito-Tooth, in the main text it also says it was paired, so I don't know what's going on with the library layout.

Thanks for going through all of these and leaving the details for me, it made reviewing so much easier!

github-actions · 2023-09-30T08:16:15Z

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_samples.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_samples.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_samples.tsv is valid

Libraries

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_libraries.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_libraries.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

github-actions · 2023-09-30T10:15:02Z

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_samples.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_samples.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_samples.tsv is valid

Libraries

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_libraries.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_libraries.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

All suggestions addressed

github-actions · 2023-10-09T10:51:58Z

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_samples.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_samples.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_samples.tsv is valid

Libraries

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_libraries.tsv is valid

Ancient Single Genome Host Associated

Invalid dataset ancientsinglegenome-hostassociated_libraries.tsv

Error	Source	Column	Row	Message
Schema Validation Error	HotStarTaq DNA Polymerase DNA	library_polymerase	2870	'HotStarTaq DNA Polymerase DNA' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

github-actions · 2023-10-09T11:42:11Z

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_samples.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_samples.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_samples.tsv is valid

Libraries

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_libraries.tsv is valid

Ancient Single Genome Host Associated

Invalid dataset ancientsinglegenome-hostassociated_libraries.tsv

Error	Source	Column	Row	Message
Schema Validation Error	HotStarTaq DNA	library_polymerase	2868	'HotStarTaq DNA' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	HotStarTaq DNA	library_polymerase	2869	'HotStarTaq DNA' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	HotStarTaq DNA	library_polymerase	2870	'HotStarTaq DNA' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	HotStarTaq DNA	library_polymerase	2871	'HotStarTaq DNA' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	HotStarTaq DNA	library_polymerase	2872	'HotStarTaq DNA' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	HotStarTaq DNA	library_polymerase	2873	'HotStarTaq DNA' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	HotStarTaq DNA	library_polymerase	2874	'HotStarTaq DNA' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	HotStarTaq DNA	library_polymerase	2875	'HotStarTaq DNA' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	HotStarTaq DNA	library_polymerase	2876	'HotStarTaq DNA' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	HotStarTaq DNA	library_polymerase	2877	'HotStarTaq DNA' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	HotStarTaq DNA	library_polymerase	2878	'HotStarTaq DNA' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	HotStarTaq DNA	library_polymerase	2879	'HotStarTaq DNA' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	HotStarTaq DNA	library_polymerase	2880	'HotStarTaq DNA' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	HotStarTaq DNA	library_polymerase	2881	'HotStarTaq DNA' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

github-actions · 2023-10-09T18:04:55Z

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_samples.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_samples.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_samples.tsv is valid

Libraries

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_libraries.tsv is valid

Ancient Single Genome Host Associated

Invalid dataset ancientsinglegenome-hostassociated_libraries.tsv

Error	Source	Column	Row	Message
Schema Validation Error	HotStarTaq DNA	library_polymerase	2868	'HotStarTaq DNA' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	HotStarTaq DNA	library_polymerase	2869	'HotStarTaq DNA' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	HotStarTaq DNA	library_polymerase	2870	'HotStarTaq DNA' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	HotStarTaq DNA	library_polymerase	2871	'HotStarTaq DNA' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	HotStarTaq DNA	library_polymerase	2872	'HotStarTaq DNA' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	HotStarTaq DNA	library_polymerase	2873	'HotStarTaq DNA' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	HotStarTaq DNA	library_polymerase	2874	'HotStarTaq DNA' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	HotStarTaq DNA	library_polymerase	2875	'HotStarTaq DNA' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	HotStarTaq DNA	library_polymerase	2876	'HotStarTaq DNA' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	HotStarTaq DNA	library_polymerase	2877	'HotStarTaq DNA' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	HotStarTaq DNA	library_polymerase	2878	'HotStarTaq DNA' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	HotStarTaq DNA	library_polymerase	2879	'HotStarTaq DNA' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	HotStarTaq DNA	library_polymerase	2880	'HotStarTaq DNA' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	HotStarTaq DNA	library_polymerase	2881	'HotStarTaq DNA' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

github-actions · 2023-10-09T18:23:05Z

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_samples.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_samples.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_samples.tsv is valid

Libraries

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_libraries.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_libraries.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

DianaSpurite · 2023-10-10T12:30:57Z

Hi Diana, Thanks for doing this! I noticed a couple of things:

For Sanganji-A1-Tooth and Sanganji-A2-Tooth, it says the polymerase is unknown- I checked the Qiagen multiplex PCR handbook, and it looks like they use a HotStarTaq polymerase, but I'm not sure if that's what they actually used.

For Deir-Rifeh-KNIII-Tooth and Deir-Rifeh-KNII-Tooth - you put half-udg but I can't find any reference to it in the original paper?

For Tepos, I think the polymerases used were Accuprime (Taq) polymerase and then further amplification with Herculase II Fusion DNA Polymerase (agilent)

For the Chincha samples, it might be best to leave the polymerase as unknown? I wasn't able to figure it out either....

For Chiribaya_Alta-Bone and El_Yaral-Bone-in the supplement, it does state it's UDG treated, so I think ok to leave as is.

Finally, for Pueblo_Bonito-Tooth, in the main text it also says it was paired, so I don't know what's going on with the library layout.

Thanks for going through all of these and leaving the details for me, it made reviewing so much easier!

I have addressed all these points, so I think it's good to go now. Thankfully, this issue was much easier than anticipated due to coordinates being available and James's suggestion to indicate exactly where in original publications the info could be found! Thank you both for your help along the process and with reviewing!

DianaSpurite · 2023-12-01T11:36:54Z

I am also requesting a review from you @alexhbnr as you are at it at the moment. This is already revised and there are comments and changes made. If you have a moment, could you please have a look and merge this also?

DianaSpurite · 2023-12-01T11:38:06Z

the sample(s?) excluded from the table here are previously sequenced

alexhbnr · 2023-12-01T12:36:04Z

I will review it properly at the beginning of next week @DianaSpurite.
I started reviewing it yesterday and realised that all DOIs are pointing to the paper by Caruana et al. instead of Hodgkins et al. I have contacted @jfy133 about how we should handle the publication DOIs of the samples as the samples have been previously published (see Supp. Data Table 2). @jfy133 pointed me to check the previous publications that had the same issue, e.g. Bieker2020 and the Oetzi publication. I will do this next week.

DianaSpurite · 2023-12-01T17:05:55Z

all DOIs are pointing to the paper by Caruana et al. instead of Hodgkins et al.

yes, that sound like my mistake, I mixed up at the beginning of working with this publication.

Thank you for looking into this, let me know if I can help.

…Dir into Caruana2013

Change publication DOI to Hodgkins2023 manuscript and sample age DOIs to the original publication reported in Hodgkins2023 Suppl. Data S2

alexhbnr · 2023-12-04T12:04:24Z

Hi @DianaSpurite and @iseultj,

I went through your review and have a few questions/comments that I am not completely sure about:

For the samples Sanganji-A1-Tooth and Sanganji-A2-Tooth, you have listed that your polymerase that was used for the library amplification was HotStarTaq DNA (see also comment by @iseultj). What I found in the Suppl. Materials is a link to this study (https://doi.org/10.1126/science.1211177) and they stated that they use two rounds of PCR amplification, one time with AmpliTaq Gold and once with Phusion. So I am puzzled how you ended up with HotStarTaq DNA instead?
For the sample Tepos_35-Tooth, there is already an entry from the original publication, so I would suggest to copy the info from there.
All references to the protocol "Meyer and Kircher, 2010" should have the "Phusion Hot Start High-Fidelity DNA" polymerase, as this is the one listed in their protocol.
For the Dacaozi-Tooth sample, the two protocols that are listed were only used for the DNA extraction steps but not for the library preparation steps. From their description of the library protocol steps, it is not apparent, which protocol they used. I would therefore propose to set it to "Unknown".

If you could please check the first question, I would then approve the review and we can merge with the master branch.

github-actions · 2023-12-04T12:04:59Z

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_samples.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_samples.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_samples.tsv is valid

Libraries

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_libraries.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_libraries.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

DianaSpurite · 2023-12-04T12:49:49Z

For the samples Sanganji-A1-Tooth and Sanganji-A2-Tooth, you have listed that your polymerase that was used for the library amplification was HotStarTaq DNA (see also comment by @iseultj). What I found in the Suppl. Materials is a link to this study (https://doi.org/10.1126/science.1211177) and they stated that they use two rounds of PCR amplification, one time with AmpliTaq Gold and once with Phusion. So I am puzzled how you ended up with HotStarTaq DNA instead?

I had set it to 'Unknown' initially, exactly because they state two, and my competence level is rather low when it comes to the sequencing methods, so I corrected it according to the review.

For the sample Tepos_35-Tooth, there is already an entry from the original publication, so I would suggest to copy the info from there.

I will check and do so.

All references to the protocol "Meyer and Kircher, 2010" should have the "Phusion Hot Start High-Fidelity DNA" polymerase, as this is the one listed in their protocol.

Can you please confirm - does this mean for Deir-Rifeh; Cueva_de_los_Lagos and Punta_Candelero samples?

For the Dacaozi-Tooth sample, the two protocols that are listed were only used for the DNA extraction steps but not for the library preparation steps. From their description of the library protocol steps, it is not apparent, which protocol they used. I would therefore propose to set it to "Unknown".

Will fix this too

If you could please check the first question, I would then approve the review and we can merge with the master branch.

alexhbnr · 2023-12-04T13:05:11Z

@DianaSpurite for points 2 to 4, I should have already done this, so nothing to worry there at the moment.
Thanks for clarifying question 1. I will wait for @iseultj's feedback and then go ahead.

Thanks @DianaSpurite for putting all the work in the first place. That was a beast of a publication to add to AMDir.

iseultj · 2023-12-04T14:51:10Z

Hi, the HotStart Taq was my mistake - I was looking at their SM where they include the following as modifications to the Rasmussen protocol: A first round PCR was set up with Multiplex PCR kit (Qiagen) as follows: 5 µl DNA library, 25 µl Mix, 20-100 nM each Multiplexing PCR primer, and H2O up to 50 µl... I looked at the multiplex PCR (qiagen) handbook to find it, but to be honest I wasn't clear whether they used the HotStart Taq or the enzymes used in the Rasmussen paper - maybe Unknown is the best way forward? Sorry for neglecting this PR, and thanks so much to both of you for both doing all the work and finishing it off!

github-actions · 2023-12-04T16:06:09Z

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_samples.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_samples.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_samples.tsv is valid

Libraries

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_libraries.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_libraries.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

github-actions · 2023-12-04T16:10:17Z

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_samples.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_samples.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_samples.tsv is valid

Libraries

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_libraries.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_libraries.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

DianaSpurite added 2 commits September 28, 2023 14:34

Update ancientsinglegenome-hostassociated_samples.tsv

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Adding Caruana2023 samples

Update ancientsinglegenome-hostassociated_libraries.tsv

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Adding Caruana2023 libraries

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Update CHANGELOG.md

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added Caruana 2023

DianaSpurite changed the title ~~Update ancientsinglegenome-hostassociated_samples.tsv~~ Caruana2023 Sep 28, 2023

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Update ancientsinglegenome-hostassociated_libraries.tsv

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Correcting library_Polymerase

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DianaSpurite requested a review from jfy133 September 28, 2023 17:41

DianaSpurite changed the title ~~Caruana2023~~ Hodgkins2023 Sep 28, 2023

Update CHANGELOG.md

ee2cdb3

Adding the correct name of the author

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Update ancientsinglegenome-hostassociated_libraries.tsv

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- added the correct author's name - corrected the last polymerase - added under-strokes in the library names for Deir-Rifeh-KNIII-Tooth and Deir-Rifeh-KNII-Tooth sample libraries

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Update ancientsinglegenome-hostassociated_samples.tsv

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replaced the wrong author with the correct one - Hodgkins2023

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Update CHANGELOG.md

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correcting author

DianaSpurite requested a review from iseultj September 28, 2023 20:52

jfy133 and others added 2 commits September 30, 2023 08:11

[skip ci] Update AncientMetagenomeDir geojson

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Merge branch 'master' into Caruana2013

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Merge branch 'master' into Caruana2013

660630a

Fix GeoJSON

818cd89

Update ancientsinglegenome-hostassociated_libraries.tsv

e9123c3

All suggestions addressed

Update ancientsinglegenome-hostassociated_libraries.tsv

7e27523

Merge remote-tracking branch 'origin/master' into Caruana2013

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DianaSpurite requested a review from alexhbnr December 1, 2023 11:37

alexhbnr added 3 commits December 4, 2023 10:08

Merge branch 'master' of github.com:SPAAM-community/AncientMetagenome…

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…Dir into Caruana2013

Change DOIs

96b3786

Change publication DOI to Hodgkins2023 manuscript and sample age DOIs to the original publication reported in Hodgkins2023 Suppl. Data S2

Update data DOI and fix library polymerases

cc118f4

Replace the polymerase with 1st one from Rasmussen et al.

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Add recent changes

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alexhbnr approved these changes Dec 4, 2023

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alexhbnr merged commit 2f80fb7 into master Dec 4, 2023
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Samples

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Ancient Metagenome Host Associated

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Samples

Ancient Metagenome Host Associated

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Ancient Metagenome Environmental

Libraries

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

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Samples

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

Libraries

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

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Samples

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

Libraries

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

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Samples

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