Project description:Urine was obtained from a patient with a urinary tract infection and frozen in 15% glycerol at -80C. For the Microcolony-seq experiment a sample from the frozen urine was serially diluted four times 10-fold and plated on an LB agar plates and incubated at 37C. After 8 hours of incubated microcolonies were visible. Twenty microcolonies were picked and subjected to the Microcolony-seq pipeline and four additional microcolonies were mixed and separated to four Eppendorf tubes and served as the technical replicates of the experiment. RNA was extracted with 1 mL TriReagent (Sigma-Aldrich) per sample. RNA quality was assessed by Nanodrop and by Bioanalyzer using the Agilent RNA 6000 Pico Kit (5067-1513). rRNA depletion was done by using the DIY rRNA depletion method, using the rRNA sequence probe set designed for E. coli K-12. RNA-seq libraries were constructed based on the RNAtag-Seq protocol with several modifications. The rRNA depletion step was done first following by the fragmentation step in the RNAtag-Seq protocol. Then the first ligation was carried out and the rest of the RNAtag-Seq protocol was followed. Libraries were single-end sequenced using the Nextseq500 Sequencer (Illumina).
Project description:To explore the classification and functional roles of bladder immune cells during urinary tract infection (UTI), we performed scRNA-seq analysis of immune cells extracted from mouse bladders.
Project description:RIVUR Trial participants had Agilent 1M probe and or Nimblegen 2.1M probe aCGH performed on genomic DNA. The study was designed to discover DNA copy number variations in genes critical in kidney/urinary tract development and urinary tract infection susceptibility. Reference DNA used is a single male sample