Data for the publication: 'Host and microbiome proteins in eco-coronas: abundance, physicochemical properties and binding partners'

This submission presents metagenomic sequencing identifications and mass-spectrometry datasets for the following publication: Brinkmann, B.W.; Zhiling, G.; Vijver, M.G..; Peijnenburg, W.J.G.M.; Chetwynd, A.J. Host and microbiome proteins in eco-coronas: abundance, physicochemical properties and binding partners. Environ. Sci.: Nano. 2025, DOI: 10.1039/d5en00493d. 1. Metagenomic sequencing identifications Tab-delimited text files with genus-level read abundances identified in whole-body metagenomes of: Daphnia magna neonates (5-6 days old): Metagenomics_Genus_Read_Abundance_Dmagna.tsv Danio rerio (5 days post-fertilization): Metagenomics_Genus_Read_Abundance_Drerio.tsv The data of both files were generated using the Pavian webtool (https://fbreitwieser.shinyapps.io/pavian/) accessed on 25 October 2024. Columns with read abudances present results for 3 biological replicates and an extraction kit metagenome (blank). The TaxId column presents the Taxonomy Identifier of NCBI Taxonomy Browser. The associated metagenomic data are deposited in the NCBI Sequence Read Archive under BioProject ID: PRJNA1336773 (http://www.ncbi.nlm.nih.gov/bioproject/1336773). 2. Proteomic datasets Tab-delimited mass-spectrometry datasets and metadata obtained for experiments with: Daphnia magna neonates (3-6 days old): Raw mass spectrometry report: MS_report_Dmagna_20241016.tsv Relative protein abundances (processed dataset): MS_relative-abundances_Dmagna.txt List with excluded accessions: MS_excluded_accessions_Dmagna.txt Acquired metadata: MS_metadata_Dmagna.txt Danio rerio (3-5 days post-fertilization): Raw mass spectrometry report: MS_report_Drerio_20241016.tsv Relative protein abundances (processed dataset): MS_relative-abundances_Drerio.txt List with excluded accessions: MS_excluded_accessions_Drerio.txt Acquired metadata: MS_metadata_Drerio.txt Sample names in the mass spectrometry datasets consist of the following three elements: {sample type}_{microbiome condition}_{replicate} where: sample type: 'medium', 'TiO2' (eco-corona), 'CNT' (eco-corona), or 'blank'. microbiome condition: 'col' for microbially colonized samples, 'GF' for germ-free samples replicate: the number of the replicate (1, 2 or 3) Accession numbers were obtained from the UniProt KB protein knowledgebase.Column names for metadata present: 'Accession', 'Genes', and 'Description' from Spectronaut mass spectrometry reports 'MultipleAcessions' indicating if there were multiple identifications (matching proteins) from the reference database Organism, protein name, taxonomy, function, gene ontologies ('GO') of three types ('GO_BP': Biological Process; 'GO_CC': Cellular Component; 'GO_MF': Molecular Function), GO IDs, keywords and keyword IDs obtained from the UniProt KB protein knowledgebase on 18 November 2024. 'Species' indicating if the protein has a 'microbial' or host ('daphnid' or 'zebrafish') origin. Predictions of total, polar and apolar solvent accessible surface area ('totalSASA', 'PolarSASA' and 'ApolarSASA', respectively) Predicted iso-electric point ('pI') and molecular weight ('MW')本数据集提交内容对应下述发表论文的宏基因组测序鉴定结果与质谱数据集： Brinkmann, B.W.; Zhiling, G.; Vijver, M.G.; Peijnenburg, W.J.G.M.; Chetwynd, A.J. 生态冠中的宿主与微生物组蛋白：丰度、理化性质与结合伴侣. 环境科学:纳米 (Environ. Sci.: Nano). 2025, DOI: 10.1039/d5en00493d. 1. 宏基因组测序鉴定结果 本部分包含基于全身体宏基因组（metagenome）鉴定得到的属水平读段丰度的制表符分隔文本文件： 大型溞（Daphnia magna）新生幼体（5-6日龄）：Metagenomics_Genus_Read_Abundance_Dmagna.tsv 斑马鱼（Danio rerio）受精后5日龄个体：Metagenomics_Genus_Read_Abundance_Drerio.tsv 上述两份文件的数据均通过Pavian网页工具（https://fbreitwieser.shinyapps.io/pavian/）于2024年10月25日生成。文件中的读段丰度列对应3次生物学重复与1次提取试剂盒宏基因组空白对照的结果。TaxId列为NCBI分类浏览器（NCBI Taxonomy Browser）的分类学标识符。相关宏基因组数据已存入NCBI序列读取存档（Sequence Read Archive, SRA），生物项目编号为PRJNA1336773（http://www.ncbi.nlm.nih.gov/bioproject/1336773）。 2. 蛋白质组数据集 本部分包含对应下述实验的制表符分隔质谱数据集与元数据： 大型溞新生幼体（3-6日龄）： - 原始质谱报告：MS_report_Dmagna_20241016.tsv - 相对蛋白丰度（处理后数据集）：MS_relative-abundances_Dmagna.txt - 排除的登录号列表：MS_excluded_accessions_Dmagna.txt - 采集的元数据：MS_metadata_Dmagna.txt 斑马鱼（受精后3-5日龄）： - 原始质谱报告：MS_report_Drerio_20241016.tsv - 相对蛋白丰度（处理后数据集）：MS_relative-abundances_Drerio.txt - 排除的登录号列表：MS_excluded_accessions_Drerio.txt - 采集的元数据：MS_metadata_Drerio.txt 质谱数据集中的样本名称由以下三部分组成：{样本类型}_{微生物组状态}_{重复编号} 其中： - 样本类型：'medium'（培养基）、'TiO2'（生态冠eco-corona）、'CNT'（生态冠eco-corona）或'blank'（空白对照） - 微生物组状态：'col'代表定殖有微生物的样本，'GF'（无菌germ-free）代表无菌样本 - 重复编号：重复次数（1、2或3） 登录号均来自UniProt蛋白质知识库（UniProt KB）。元数据的列名包括： - 来自Spectronaut质谱报告的'Accession'（登录号）、'Genes'（基因）与'Description'（描述） - 'MultipleAccessions'：指示参考数据库中是否存在多个匹配蛋白的鉴定结果 - 2024年11月18日从UniProt KB获取的信息：生物体、蛋白名称、分类学信息、功能、三类基因本体（Gene Ontology, GO）：GO_BP（生物过程 Biological Process）、GO_CC（细胞组分 Cellular Component）、GO_MF（分子功能 Molecular Function）、GO编号、关键词与关键词编号 - 'Species'：指示蛋白来源于微生物还是宿主（大型溞daphnid或斑马鱼zebrafish） - 总、极性与非极性溶剂可及表面积的预测值（分别为totalSASA、PolarSASA与ApolarSASA） - 预测的等电点（iso-electric point, pI）与分子量（molecular weight, MW）