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Fioriin2024 samples #1149

Merged
merged 13 commits into from
Mar 28, 2024
Merged

Fioriin2024 samples #1149

merged 13 commits into from
Mar 28, 2024

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jfy133
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@jfy133 jfy133 commented Mar 22, 2024 •
edited by rozwalak
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Pull Request

This PR is for a

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 #1141

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:

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jfy133 commented Mar 22, 2024

@spaam-bot autofill ancientmetagenome-hostassociated Fioriin2024

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jfy133 commented Mar 22, 2024

@spaam-bot please autofill ancientmetagenome-hostassociated Fioriin2024

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jfy133 commented Mar 22, 2024

@spaam-bot please autofill ancientmetagenome-hostassociated Fiorin2024

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jfy133 commented Mar 22, 2024

@spaam-bot please autofill ancientmetagenome-hostassociated Fiorin2024

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jfy133 commented Mar 22, 2024

@spaam-bot please autofill ancientmetagenome-hostassociated Fiorin2024

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jfy133 commented Mar 22, 2024

@spaam-bot please autofill ancientmetagenome-hostassociated Majander2024

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jfy133 commented Mar 22, 2024

@spaam-bot please autofill ancientsinglegenome-hostassociated Majander2024

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jfy133 commented Mar 25, 2024

@spaam-bot please autofill ancientmetagenome-hostassociated Fiorin2024

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jfy133 commented Mar 25, 2024

@spaam-bot please autofill ancientmetagenome-hostassociated Fiorin2024

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jfy133 commented Mar 25, 2024

@spaam-bot please autofill ancientmetagenome-hostassociated Fiorin2024

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jfy133 commented Mar 25, 2024

@spaam-bot please autofill ancientmetagenome-hostassociated Fiorin2024

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jfy133 commented Mar 25, 2024

@spaam-bot please autofill ancientmetagenome-hostassociated Fiorin2024

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jfy133 commented Mar 25, 2024

@spaam-bot please autofill ancientmetagenome-hostassociated Fiorin2024

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jfy133 commented Mar 25, 2024

@spaam-bot please autofill ancientmetagenome-hostassociated Fiorin2024

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jfy133 commented Mar 25, 2024

@spaam-bot please autofill ancientmetagenome-hostassociated Fiorin2024

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jfy133 commented Mar 25, 2024

@spaam-bot please autofill ancientmetagenome-hostassociated Fiorin2024

alexhbnr
alexhbnr approved these changes Mar 27, 2024
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I reviewed the study but made two changes:

  1. For the samples, the phase I was assigned to the mid 12th century so I put the sample age of 900 instead of 1800. ("... of which 38 related to the first phase of use at the site up to the mid-12th century...")
  2. For the libraries, the authors explicitly state in the Suppl. Material which polymerase they used for indexing: "A total of 15 μL of each library were split in three reactions and used as a template in 50 μL volume for double-indexing PCR (25 cycles; PfuTurbo Cx Hotstart polymerase 0.05 U/μL...". I therefore also changed the polymerase.

Otherwise, it looks fine to me.

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AMDirT, version 1.5.0

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

@jfy133 jfy133 merged commit 43b3c8f into master Mar 28, 2024
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@jfy133 jfy133 deleted the Fiorin2024 branch March 28, 2024 13:38
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Fiorin2024
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