biostudies-arrayexpressMahesh Shrinivasan IyerApilactobacillus kunkeeihttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16234This study aims to profile small RNA expression in three wild-type Apilactobacillus kunkeei (A1401, H3B2-02X and H2B1-05J) strains during mid-exponential growth. Cultures were harvested at OD 0.5–0.6, and total RNA was purified for small RNA sequencing. UMI-based small RNA libraries were generated with size selection of RNA fragments approximately 17–200 nt and sequenced using 50-bp single-end reads on the DNBSEQ platform. The dataset provides strain-specific small RNA expression profiles based on three biological replicates per strain.biostudies-arrayexpressLibrary Construction - Small RNA sequencing libraries were prepared at BGI Genomics using a UMI small RNA library preparation kit. RNA fragments of approximately 17–200 nt were size-selected according to the manufacturer’s instructions. Adapter ligation and UMI incorporation were performed during library construction. The final libraries were quality-checked and quantified before sequencing.Sample Collection - Cultures were grown statically in MRS medium supplemented with 5% fructose at 35 °C. Cells were harvested during mid-exponential growth (OD600 0.5–0.6) by centrifugation and immediately stabilized in RNAlater. Samples were stored and transported on dry ice prior to RNA extraction.Nucleic Acid Extraction - Cell pellets corresponding to 10 OD units were lysed in TRIzol using a handheld homogenizer. Total RNA was purified using the Ribo-Pure RNA extraction kit (Thermo Fisher), followed by DNase digestion. RNA quality and integrity were assessed prior to library preparation.Sequencing - Small RNA libraries were sequenced by BGI Genomics using the DNBSEQ platform, generating 50 bp single-end, unstranded reads. Sequencing was performed according to manufacturer-recommended protocols. Data were delivered in demultiplexed FASTQ format with adapter and low-quality reads removed.OrganizationMINSEQE ScoreAssays and DataMAGE-TAB FilesSequence Alignment - Adapter trimming and quality filtering were performed by the sequencing provider, removing reads shorter than 15 nt. Clean reads were aligned to the respective Apilactobacillus kunkeei reference genomes using Bowtie2 with default parameters. Aligned reads were visualized using Tablet genome viewer. Coverage plots for small RNA features (including crRNA and tracrRNA loci) were generated using custom Python scripts.UnknownTranscriptomicsGenomicsProteomicsDNBSEQ-G400Handheld homogenizer, centrifugeComputer WorkstationIncubator at 35 °C, centrifugeUMI small RNA library preparation kit (BGI)RNA-seq of non coding RNAApilactobacillus kunkeeiSiv AnderssonMahesh Shrinivasan IyerfalseSmall RNA-seq profiling of wild-type Apilactobacillus kunkeei strains in mid-exponential phase using UMI-based librariesThis study aims to profile small RNA expression in three wild-type Apilactobacillus kunkeei (A1401, H3B2-02X and H2B1-05J) strains during mid-exponential growth. Cultures were harvested at OD 0.5–0.6, and total RNA was purified for small RNA sequencing. UMI-based small RNA libraries were generated with size selection of RNA fragments approximately 17–200 nt and sequenced using 50-bp single-end reads on the DNBSEQ platform. The dataset provides strain-specific small RNA expression profiles based on three biological replicates per strain.2026-05-01T00:00:00Z2026-05-01T01:03:25.293Z2025-11-20T19:30:36.699ZE-MTAB-16234ERP185436EFO_0003737EFO_0002944EFO_0004170EFO_0004917EFO_0005518EFO_0004184