2026-10-07T16:35:48Z https://api.figshare.com/v2/oai

oai:figshare.com:article/31455268 2026-09-28T15:47:24Z category_26269 category_24343 item_type_3 month_year_09_2026

Machine-learning guided discovery of emergent antimicrobial activity from dynamic covalent assemblies（Holstein cattle， RNA seq） Yuanfeng Li (21088505) Ji-yang Chen (22490594) Yinzi Piao (21088633) Zhanpei Bai (23291914) haoyue wu (22105418) Yu-han Zhao (23291972) Yuqin Wang (23291993) Haibo Zhang (5061767) Xiufeng Huang (2887607) Tieli Zhou (129625) Jian Li (41607) Linqi Shi (21088642) Yong Liu (19677156) Biomaterials Nanobiotechnology machine-learning functions Nanobiotechnology -- Research <p dir="ltr">This dataset contains host bulk RNA-seq data and uterine microbiome 2bRAD-M data from a Holstein dairy cow study of naturally occurring endometritis. The RNA-seq component includes 12 uterine wall tissue samples: Healthy, PBS-treated endometritis controls, A5B5-treated samples and antibiotic-treated samples, with three biological replicates per group. counts_anno.csv and FPKM_anno.csv each contain all 12 samples in one annotated expression matrix comprising 22,314 gene identifiers shared by the source datasets. sample_metadata.csv defines the RNA-seq sample groups.</p><p dir="ltr"><br></p><p dir="ltr">The microbiome component includes 21 biological samples: Healthy, PBS and A5B5 groups with six samples each, and an oxytetracycline group with three samples. All 21 samples are included in Abundance.filtered.anno.csv as a single annotated species-level relative-abundance matrix. 2bRADM_sample_metadata.csv defines the groups and identifies the 12 samples used in the current four-group analysis (three per group). Vendor reference/control columns are excluded from biological sample matrices.</p><p dir="ltr"><br></p><p dir="ltr">Methods documented for the original samples: Total RNA was extracted using TRIzol according to the manufacturer’s protocol; RNA quantity and purity were assessed using NanoDrop 2000, and RNA integrity was assessed using the Agilent 2100 Bioanalyzer. Libraries were prepared with the VAHTS Universal V10 RNA-seq Library Prep Kit (Premixed Version) and sequenced on an Illumina NovaSeq 6000 platform to generate 150 bp paired-end reads. Raw FASTQ data were processed with fastp for quality control and adapter/low-quality read removal, and clean reads were aligned to the reference genome using HISAT2. Gene-level read counts were obtained with HTSeq-count, and expression abundance was calculated (FPKM).</p> 2026-03-04T05:57:29Z Dataset Dataset 10.6084/m9.figshare.31455268.v2 https://figshare.com/articles/dataset/Machine-learning_guided_discovery_of_emergent_antimicrobial_activity_from_dynamic_covalent_assemblies_Holstein_cattle_RNA_seq_/31455268 CC BY 4.0