The North Pacific Eukaryotic Gene Catalog: Raw assemblies from Gradients 1, 2 and 3

The North Pacific Eukaryotic Gene Catalog consolidates eukaryotic metatranscriptome data from three latitudinal transects of the North Pacific transition zone and one cruise in the subtropical gyre. Metatranscriptomes were gathered from latitudinally-resolved surface samples, and diel-resolved temporal studies, with samples taken in triplicate or duplicate and collected on 0.2-100 μm, 0.2-3 μm, and 3 μm-100 or 200 μm size fractions. These metatranscriptome data were de novo assembled into 175 independent assemblies, totalling 182 million clustered nucleotide contigs. Assemblies were annotated by taxonomy and function. This catalog provides assembled environmental contigs, their translated peptide sequences, and their taxonomic and functional annotations with the aim of facilitating continued discoveries about the molecular ecology of microbial eukaryotes in the North Pacific.A full description of this data is published in Scientific Data, available here: The North Pacific Eukaryotic Gene Catalog of metatranscriptome assemblies and annotations. Please cite this publication if your research uses this data:Groussman, R. D., Coesel, S. N., Durham, B. P., Schatz, M. J., & Armbrust, E. V. (2024). The North Pacific Eukaryotic Gene Catalog of metatranscriptome assemblies and annotations. Scientific Data, 11(1), 1161. This dataset repository is associated with a codebase and documentation repository:https://github.com/armbrustlab/NPac_euk_gene_catalogPlease see this code repository for additional data and project updatesTranslated and processed protein sequences and their annotations are available in this repository: https://zenodo.org/doi/10.5281/zenodo.1047258999% identity clustered nucleotide sequences and kallisto enumerations are available here:https://zenodo.org/doi/10.5281/zenodo.10570448 File contents: this repository contains five .tar.gz compressed tarballs with raw de novo Trinity assemblies of poly-A selected metatranscriptomes from the Gradients 1 through 3 cruises, and a plain-text file with the custom spike-in mRNA standards (CustomStandardSequences.txt) Gradients1.KOK1606.PA.assemblies.tar.gz- Link to G1PA project github page- Simons CMAP cruise page and datasets: https://simonscmap.com/catalog/cruises/KOK1606- Short read processing code: G1PA.process_short_reads.sh- Trinity assembly code: G1PA.trinity_assemblies.sh Gradients2.MGL1704.PA.assemblies.tar.gz- Link to G2PA project github page- Simons CMAP cruise page and datasets: https://simonscmap.com/catalog/cruises/MGL1704- Short read processing code: G2PA.process_short_reads.sh- Trinity assembly code: G2PA.trinity_assemblies.sh Gradients3.KM1906.PA.assemblies.tar.gz- Link go G3PA project github page- Simons CMAP cruise page and datasets: https://simonscmap.com/catalog/cruises/KM1906- Short read processing code: G3PA_UW.process_short_reads.sh- Trinity assembly code: G3PA_UW.trinity_assemblies.sh G3_diel.KM1906.PA.assemblies.tar.gz- Link go G3PA project github page- Simons CMAP cruise page and datasets: https://simonscmap.com/catalog/cruises/KM1906- Short read processing code: G3PA_diel.process_short_reads.sh- Trinity assembly code: G3PA_diel.trinity_assemblies.sh CustomStandardSequences.txt- Plain-text FASTA file with the spike-in standards used during mRNA extraction and sequencing prep- Link to publication of spike-in standards methods: https://www.nature.com/articles/s41564-019-0507-5 The 2015 SCOPE Diel metatranscriptome raw assemblies have been released in a previous Zenodo repository, and are not included again in this deposition. We provide the links to the Diel1 resources here:- Diel1 raw metatranscriptome assembly Zenodo repository: https://zenodo.org/records/5009803- Dataset DOI: https://doi.org/10.5281/zenodo.5009803- Associated publication: https://www.frontiersin.org/articles/10.3389/fmicb.2021.682651/full- Codebase: https://github.com/armbrustlab/diel_eukaryotes- Simons CMAP cruise page and datasets: https://simonscmap.com/catalog/cruises/KM1513- Short read processing code: D1PA.process_short_reads.sh- Trinity assembly code: D1PA.trinity_assemblies.sh北太平洋真核基因目录（North Pacific Eukaryotic Gene Catalog）整合了北太平洋过渡带三个纬度断面以及亚热带环流区一次航次的真核宏转录组（metatranscriptome）数据。宏转录组数据采集自经纬度解析的表层样本与昼夜节律解析的时序样本，样本设置三次或两次生物学重复，采集于0.2–100 μm、0.2–3 μm以及3 μm–100或200 μm的粒径分级滤膜上。上述宏转录组数据经从头组装得到175个独立组装结果，总计包含1.82亿条聚类后的核苷酸重叠群（contig）。组装结果已完成分类学与功能注释。本目录提供组装得到的环境重叠群、其翻译得到的肽序列，以及对应的分类学与功能注释，旨在推动北太平洋微生物真核生物分子生态学领域的后续研究发现。 本数据集的完整描述已发表于《Scientific Data》（科学数据），原文标题为《The North Pacific Eukaryotic Gene Catalog of metatranscriptome assemblies and annotations》，可通过对应渠道获取。若您的研究使用本数据集，请引用以下文献：Groussman, R. D., Coesel, S. N., Durham, B. P., Schatz, M. J., & Armbrust, E. V. (2024). The North Pacific Eukaryotic Gene Catalog of metatranscriptome assemblies and annotations. Scientific Data, 11(1), 1161. 本数据集仓库关联了代码库与文档仓库：https://github.com/armbrustlab/NPac_euk_gene_catalog。如需获取额外数据与项目更新，请查阅该代码仓库。 翻译并经过处理的蛋白质序列及其注释可在以下仓库获取：https://zenodo.org/doi/10.5281/zenodo.1047258999；99%一致性聚类核苷酸序列与kallisto计数结果可在此处获取：https://zenodo.org/doi/10.5281/zenodo.10570448 文件内容：本仓库包含5个.tar.gz压缩tar包，内含Gradients 1至3航次经poly-A富集的宏转录组的从头Trinity（Trinity）组装结果，以及一个包含自定义内参mRNA标准序列的纯文本文件（CustomStandardSequences.txt）。 Gradients1.KOK1606.PA.assemblies.tar.gz： - 关联G1PA项目的GitHub页面链接 - Simons CMAP（Simons CMAP）航次页面与数据集：https://simonscmap.com/catalog/cruises/KOK1606 - 短读长处理代码：G1PA.process_short_reads.sh - Trinity组装代码：G1PA.trinity_assemblies.sh Gradients2.MGL1704.PA.assemblies.tar.gz： - 关联G2PA项目的GitHub页面链接 - Simons CMAP航次页面与数据集：https://simonscmap.com/catalog/cruises/MGL1704 - 短读长处理代码：G2PA.process_short_reads.sh - Trinity组装代码：G2PA.trinity_assemblies.sh Gradients3.KM1906.PA.assemblies.tar.gz： - 关联G3PA项目的GitHub页面链接 - Simons CMAP航次页面与数据集：https://simonscmap.com/catalog/cruises/KM1906 - 短读长处理代码：G3PA_UW.process_short_reads.sh - Trinity组装代码：G3PA_UW.trinity_assemblies.sh G3_diel.KM1906.PA.assemblies.tar.gz： - 关联G3PA项目的GitHub页面链接 - Simons CMAP航次页面与数据集：https://simonscmap.com/catalog/cruises/KM1906 - 短读长处理代码：G3PA_diel.process_short_reads.sh - Trinity组装代码：G3PA_diel.trinity_assemblies.sh CustomStandardSequences.txt： - 包含mRNA提取与建库过程中使用的内参标准序列的纯文本FASTA（FASTA）文件 - 内参标准方法相关发表文献链接：https://www.nature.com/articles/s41564-019-0507-5 2015年SCOPE昼夜宏转录组原始组装结果已在之前的Zenodo（Zenodo）仓库发布，本次上传未重复包含。此处提供Diel1资源的相关链接： - Diel1原始宏转录组组装Zenodo仓库：https://zenodo.org/records/5009803 - 数据集DOI：https://doi.org/10.5281/zenodo.5009803 - 关联发表文献：https://www.frontiersin.org/articles/10.3389/fmicb.2021.682651/full - 代码库：https://github.com/armbrustlab/diel_eukaryotes - Simons CMAP航次页面与数据集：https://simonscmap.com/catalog/cruises/KM1513 - 短读长处理代码：D1PA.process_short_reads.sh - Trinity组装代码：D1PA.trinity_assemblies.sh