2026-10-07T14:57:58Z https://api.figshare.com/v2/oai

oai:figshare.com:article/31454647 2026-09-28T15:47:15Z category_26269 category_24343 item_type_3 month_year_09_2026

Machine-learning guided discovery of emergent antimicrobial activity from dynamic covalent assemblies（<i>Escherichia coli</i>， 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 biotechnology platform <p dir="ltr">This dataset contains bulk RNA-seq data from Escherichia coli under four conditions: PBS control, A5B5 treatment for 0.5 h at a sub-MIC concentration, A5B5 treatment for 4 h, and chlorhexidine (CHX) treatment, with three biological replicates per condition (12 samples in total). counts_anno.csv and FPKM_anno.csv each contain all 12 samples in one annotated expression matrix comprising 4,192 gene identifiers present in both source datasets. AB5-1/2/3 are the A5B5 4-h samples, A5B5_0.5h-1/2/3 are the added 0.5-h samples, and CHX1-1/2/3 are the CHX samples. sample_metadata.csv provides sample groups and original identifiers.</p><p dir="ltr"><br></p><p dir="ltr">Methods documented for the original samples: Total RNA was extracted from bacterial samples using a bacterial RNA extraction workflow, and ribosomal RNA was depleted using the TIANSeq rRNA Depletion Kit (G-Bacteria). The remaining RNA was fragmented and used for first-strand cDNA synthesis with random hexamer primers. Strand-specific libraries were generated through dUTP-based second-strand synthesis followed by UNG digestion, and then processed through adapter ligation, purification, end repair, A-tailing, size selection, and PCR amplification. Library quality was evaluated using an Agilent 2100 Bioanalyzer, and qualified libraries were sequenced on an Illumina platform (paired-end RNA-seq).</p> 2026-03-04T05:59:54Z Dataset Dataset 10.6084/m9.figshare.31454647.v2 https://figshare.com/articles/dataset/Machine-learning_guided_discovery_of_emergent_antimicrobial_activity_from_dynamic_covalent_assemblies_i_Escherichia_coli_i_RNA_seq_/31454647 CC BY 4.0