Amplicon Gradients 1-3: North Pacific Ocean Datasets

Subtitle
North Pacific amplicon sequencing and metadata (2016–2019)

Description

This project contains Qiime2 (v2022.8) processed amplicon sequencing data (16S and 18S rRNA gene ASVs) with associated metadata from three North Pacific Ocean surveys: Gradients 1 (2016), Gradients 2 (2017), and Gradients 3 (2019). Dataframes provided in this Zenodo entry have not been rarefied yet via Phyloseq.

Publication Info

• "Picophytoplankton Implicated in Productivity and BiogeoChemistry in the North Pacific transition Zone". Preprint DOI: https://doi.org/10.1101/2025.05.29.656823 . Journal DOI: TBA

External Data Repositories

• Raw amplicon sequences: NCBI BioProject PRJNA1302492 

• R and Bash scripts:  Rebecca Key’s GitHub

• Processed dataframes are also accessible through Simon's CMAP data portal: 
  • G1_CMAP_Catalog 
  • G2_CMAP_Catalog
  • G3_CMAP_Catalog

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Datasets

• There are 6 compressed files: 

  • G1_Prok.tar.gz

  • G1_Euk.tar.gz

  • G2_Prok.tar.gz

  • G2_Euk.tar.gz

  • G3_Prok.tar.gz

  • G3_Eukj.tar.gz

⚠️ Each tar.gz file contains 3 dataframes: a count table, taxonomy table, and sample metadata. The sample metadata will contain latitude/longitude coordinates, station, depth (meters), filter type, and collection times. The Taxonomy file will also contain ASV sequences. Counts have not been rarified

• 3 CMAP-formatted files: 

  • G1_ASVs_CMAP_Format.xlxs

  • G2_ASVs_CMAP_Format.xlxs

  • G3_ASvs_CMAP_Format.xlxs

⚠️ Each .xlxs file contains the 'master' dataframe (ie. the count table, tax table, and sample metadata is already merged for you). There are two extra tabs: additional meta info and explanations for each column in the master. Counts have not been rarified

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Notes For Users

• Prokaryote Taxonomy = SILVA database v138.1, Primer Set 515F/806R;  V4 rRNA region
• Eukaryote Taxonomy = PR2 database v5.1, Primer Set 566F/1200R; V4-V5 rRNA region (Note: only the 566F read was used, taxonomy is based on V4 only! See Key RS. et al. 2025 supplement for more info

🆘 Questions??

Please reach out to Rebecca Key (rkeyMicrobe[at]proton[dot]me) or Bryndan Durham (b[dot]durham[at]ufl[dot]edu)

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History Log for Creators

* Hx.2025-09-25.rsk: Added CMAP versions. Non-CMAP versions remain unchanged. Manual archive by Zenodo Support team. V1 record

* Hx.2025-09-26.rsk: Created a Zenodo DOI. V2. Prior DOI linked to preprint. Old record: https://zenodo.org/records/16878708. Provided an update to G3_CMAP_format, flagged by CMAP Support Team. Non-CMAP versions remain unchanged

* Hx.2025-10-06.rsk: Zenodo-CMAP must be same per CMAP Support. G3 longitude: pos to neg #s. G1-3 Colname: depth_m to depth. G1-3 descr: less redudancy. New version created, V3. Non-CMAP versions remain unchanged

*Hx.2025-10-07.rsk: Final G3 excel Mods from CMAP Support. Numeric depth col + original col w/ character observations. V4