Project description:This study investigates the gut microbiome composition and diversity in three groups of rats: control, radiation enteritis model, and treatment (TG) groups. Total DNA was extracted from stool samples, PCR-amplified targeting 16S rRNA gene variable regions, and sequenced using Illumina MiSeq or NovaSeq platforms. Downstream bioinformatics analyses included sequence quality control, denoising (DADA2/OTU clustering), taxonomic classification, alpha and beta diversity evaluation, differential species abundance analysis, and functional prediction. The processed data include ASV/OTU tables, taxonomy assignments, and sample metadata.
Project description:Nitrate-reducing iron(II)-oxidizing bacteria are widespread in the environment contribute to nitrate removal and influence the fate of the greenhouse gases nitrous oxide and carbon dioxide. The autotrophic growth of nitrate-reducing iron(II)-oxidizing bacteria is rarely investigated and poorly understood. The most prominent model system for this type of studies is enrichment culture KS, which originates from a freshwater sediment in Bremen, Germany. To gain insights in the metabolism of nitrate reduction coupled to iron(II) oxidation under in the absence of organic carbon and oxygen limited conditions, we performed metagenomic, metatranscriptomic and metaproteomic analyses of culture KS. Raw sequencing data of 16S rRNA amplicon sequencing, shotgun metagenomics (short reads: Illumina; long reads: Oxford Nanopore Technologies), metagenome assembly, raw sequencing data of shotgun metatranscriptomes (2 conditions, triplicates) can be found at SRA in https://www.ncbi.nlm.nih.gov/bioproject/PRJNA682552. This dataset contains proteomics data for 2 conditions (heterotrophic and autotrophic growth conditions) in triplicates.
Project description:Purpose: The goal of this study is to compare endothelial small RNA transcriptome to identify the target of OASL under basal or stimulated conditions by utilizing miRNA-seq. Methods: Endothelial miRNA profilies of siCTL or siOASL transfected HUVECs were generated by illumina sequencing method, in duplicate. After sequencing, the raw sequence reads are filtered based on quality. The adapter sequences are also trimmed off the raw sequence reads. rRNA removed reads are sequentially aligned to reference genome (GRCh38) and miRNA prediction is performed by miRDeep2. Results: We identified known miRNA in species (miRDeep2) in the HUVECs transfected with siCTL or siOASL. The expression profile of mature miRNA is used to analyze differentially expressed miRNA(DE miRNA). Conclusions: Our study represents the first analysis of endothelial miRNA profiles affected by OASL knockdown with biologic replicates.
Project description:Circadian clocks are important for gut health. This experiment aimed to determine the role of core clock gene Bmal1 in regulating microbial rhythmicity in health and dextran sulphate sodium induced colitis. Mice were generated with Bmal1 selectively deleted in Villin-expressing cells (predominantly IECs).Microbial DNA was extracted from fecal pellets collected from IEC-Bmal1-/- and Bmal1flox mice (aged 8-19 weeks) at zeitgeber time 0, 4, 8, 12, 16, 20 across the 24h day with the DNeasy PowerSoil Pro Kit (Qiagen), as per manufacturer’s instructions. Pre-amplification of the V4 region of 16S rRNA was performed using forward primer 5'-ACACTCTTTCCCTACACGACGCTCTTCCGAT-CTNNNNNGTGCCAGCMGCCGCGGTAA-3' (annealing sites in bold) and reverse primer 5'-GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGGACTACHVGGGTWTCTAAT-3'. Sequencing was performed by the University of Liverpool Centre for genomics Research, using the Illumina MiSeq v2 platform (Illumina), generating 250bp paired-end reads. PhiX control v3 library (PhiX) was spiked into samples to balance low base diversity often found in microbiome samples. Quality control was performed and OTU tables were generated using a pipeline provided by the University of Manchester Bioinformatics Core Facility local Galaxy service. Briefly, VSEARCH clustered OTUs and removed chimeras. The OTU database was mapped to the SILVA (v138) reference database with >97% homology threshold. All samples passed quality checks and had sequence depth >45,000. The OTU table was analysed using R packages phyloseq, vegan, limma and ALDEx2. JTK_CYCLE 93 was used to identify rhythmic OTUs with a period of 24 h and an adjusted P value < 0.05.