https://researchdata.se/sv/catalogue Search results sv The study aimed to improve the speed of drug susceptibility testing for tuberculosis (TB), particularly drug-resistant strains. Current phenotypic drug susceptibility testing (pDST) methods take at least two weeks. This study used microfluidic chips, microscopy, and deep neural network algorithms to monitor the growth of Mycobacterium bovis Bacillus Calmette–Guérin (BCG) and Mycobacterium smegmatis in the presence of antibiotics. The findings suggest that pDST for TB could potentially be completed in less than 12 hours for slow-growing mycobacteria, offering a significant improvement in diagnosing drug-resistant TB. The entry contains raw microscopy data, analysis code and output, and code to generate figures. Mon, 15 Dec 2025 00:00:00 GMT https://researchdata.se/sv/catalogue/dataset/doi-10-17044-scilifelab-26927146 https://researchdata.se/sv/catalogue/dataset/doi-10-17044-scilifelab-26927146 Uppsala universitet Buu Minh Tran Jimmy Larsson Anastasia Grip Praneeth Karempudi Johan Elf Transcriptomic data raw reads and differential expression (DE) analysis comparing induced cdiA-CTo11 toxin to an empty vector control after induction for 0, 5 or 20 minutes. This dataset contains both raw reads and differential expression analysis for three biological replicates, together making up all transcriptomic data shown in the publication A delivered DNase toxin creates population heterogeneity through transient intoxication of siblings, DOI 10.1128/mbio.02083-25. Mon, 29 Sep 2025 00:00:00 GMT https://researchdata.se/sv/catalogue/dataset/doi-10-17044-scilifelab-30084340 https://researchdata.se/sv/catalogue/dataset/doi-10-17044-scilifelab-30084340 Uppsala universitet Hanna Eriksson Susan Schlegel Sanna Koskiniemi S. coelicolor was inoculated on FAM and incubated for 20 days at 30°C, to allow for sectors to form. the sectors were isolated and grown in TSB media and 600 mg pellet was collected and sent to MicrobesNG for DNA preparation and Illumina sequencing. Trimmed (Trimmomatic) and quality checked reads (using MicrobesNG in-house scripts combined with Samtools BedTools, and bwa-mem) were returned for (i) inoculum "WTparental", (ii) first level sector "alpha"/"A0", (iii) second levels sectors "I"/"A1" and "IV"/"A4". Thu, 25 Apr 2024 00:00:00 GMT https://researchdata.se/sv/catalogue/dataset/doi-10-17044-scilifelab-25593405 https://researchdata.se/sv/catalogue/dataset/doi-10-17044-scilifelab-25593405 Umeå universitet Linda Sandblad Niklas Söderholm For the nutrient analysis of agar, six replicates of agar plugs were collected from the edge of the dish and 0.5 cm away from the S. coelicolor colonies on 0.5xTSA medium. This sampling was performed on six different ⌀ 4 cm plates. Three control samples were taken at every time point from three sterile 0.5xTSA dishes. Sample preparation was performed according to A et al. (A et al., 2005). The samples were stored at -80 °C until analysis. Small aliquots of the remaining supernatants were pooled and used to create quality control (QC) samples. The samples were analyzed in batches according to a randomized run order on GC-MS. Derivatization and GCMS analysis were performed as described previously A et al. (A et al., 2005). Non-processed MS-files from the metabolic analysis were exported from the ChromaTOF software in NetCDF format to MATLAB-R2020a (Mathworks, Natick, MA, USA), where all data pre-treatment procedures (base-line correction, chromatogram alignment, data compression and Multivariate Curve Resolution) were performed. The extracted mass spectra were identified by comparisons of their retention index and mass spectra with libraries of retention time indices and mass spectra (Schauer et al., 2005). Mass spectra and retention index comparison was performed using NIST MS 2.2 software. Annotation of mass spectra was based on reverse and forward searches in the library. Masses and ratio between masses indicative of a derivatized metabolite were especially notified. The mass spectrum with the highest probability indicative of a metabolite and the retention index between the sample and library for the suggested metabolite was ± 5 the deconvoluted “peak” was annotated as an identification of a metabolite. Thu, 25 Apr 2024 00:00:00 GMT https://researchdata.se/sv/catalogue/dataset/doi-10-17044-scilifelab-25593480 https://researchdata.se/sv/catalogue/dataset/doi-10-17044-scilifelab-25593480 Umeå universitet Linda Sandblad Niklas Söderholm For untargeted metabolite analysis, agar stubs were punched out from just outside of S. coelicolor colonies on FAM and FAM+G. For each condition, twelve samples were isolated from plates inoculated with S. coelicolor, in addition to two control samples each from sterile plates. The weight of the samples were adjusted to 100 mg before the addition of 1 mL extraction buffer (90/10 v/v methanol:water). Internal standards (13C9-Phenylalanine, 13C3-Caffeine was, D4-Cholic acid, D8-Arachidonic Acid, 13C9-Caffeic Acid) were added to each sample. The sample was shaken at 30 Hz for 3 min in a mixer mill, and proteins were precipitated at +4 °C for 2h on ice. The sample was centrifuged at +4 °C, 14 000 rpm, for 10 min. The supernatant was transferred to a microvial and solvents evaporated. Before analysis, the sample was re-suspended in 10 + 10 µL methanol and water. The set of samples were analyzed in positive mode and negative mode. The chromatographic separation was performed on an Agilent 1290 Infinity UHPLC-system (Agilent Technologies, Waldbronn, Germany). Re-suspended aliquots (2 µL) of the agar extracts were injected onto an Acquity UPLC HSS T3, 2.1 x 50 mm, 1.8 µm C18 column in combination with a 2.1 mm x 5 mm, 1.8 µm VanGuard precolumn (Waters Corporation, Milford, MA, USA) held at 40°C. The gradient elution buffers were A (H2O, 0.1 % formic acid) and B (75/25 acetonitrile:2-propanol, 0.1 % formic acid). The compounds were detected with an Agilent 6550 Q-TOF mass spectrometer equipped with a jet stream electrospray ion source. The settings were kept identical between the modes, except the capillary voltage. The data processing was performed using the Recursive Feature Extraction algorithm within Agilent Masshunter Profinder version B.08.00 (Agilent Technologies Inc., Santa Clara, CA, USA). All multivariate statistical investigations (PCA) were performed using the software package SIMCA®-P+ version 15.0.2 (Umetrics, Umeå, Sweden). Thu, 25 Apr 2024 00:00:00 GMT https://researchdata.se/sv/catalogue/dataset/doi-10-17044-scilifelab-25593528 https://researchdata.se/sv/catalogue/dataset/doi-10-17044-scilifelab-25593528 Umeå universitet Linda Sandblad Niklas Söderholm Supplementary information for manuscript "Apilactobacillus kunkeei releases RNA-associated membrane vesicles and proteinaceous nanoparticles". The supplementary information comprises imaging data obtained from Transmission (TEM) and Scanning Electron Microscopy (SEM) as well as negative stain TEM (nsTEM). Electron micrographs have been obtained from whole cells of two Apilactobacillus kunkeei strains, A0901 and A1401, by TEM and SEM, as well as from isolated secreted nanoparticles (nSTEM). Those particles have been described as membranous RNA-associated membrane vesicles (MVs) and proteinaceous extracellular particles (ECPs). The compressed folder contains the imaging files. Files and subdirectories are described in manifest.txt. The imaging folder contains a file, file.description.ecp.imaging.xlsx, with metainformation on the collected electron microscopy images. Mon, 11 Sep 2023 00:00:00 GMT https://researchdata.se/sv/catalogue/dataset/doi-10-17044-scilifelab-20749174 https://researchdata.se/sv/catalogue/dataset/doi-10-17044-scilifelab-20749174 Uppsala universitet Christian Seeger Karl Dyrhage Kristina Näslund Siv Andersson Experimental data description All experiments performed are timelapse microscopy experiments. Each experiment contains two directories, one containing phase contrast images arranged by positions on the microfluidic device, and the other contains the analysis scripts. The 'Overview.csv' file contains a full description for the conditions in each experiment. Experiments can be divided into 3 categories: 1. 4h exposure to various antibiotics (E. coli) These are the main experiments within the paper where cells are exposed to various antibiotics at 1/8x, 1/4x, 1/2x and 1x MIC.   a) EXP-21-BW5663_LB-1.zip (LB replicate 1) b) EXP-22-BY2422_LB-2.zip (LB replicate 2) c) EXP-21-BW5667_CAR-1.zip (CAR replicate 1) d) EXP-22-BY1020_CAR-2.zip (CAR replicate 2) e) EXP-21-BT2897_CRO-1.zip (CRO replicate 1) f) EXP-22-BY2425_CRO-2.zip (CRO replicate 2) g) EXP-21-BY1007_CHL-1.zip (CHL replicate 1) h) EXP-22-BY1043_CHL-2.zip (CHL replicate 2) i) EXP-21-BT2896_CIP-1.zip (CIP replicate 1) j) EXP-22-BY2424_CIP-2.zip (CIP replicate 2) k) EXP-21-BW5664_GEN-1.zip (GEN replicate 1) l) EXP-22-BY1022_GEN-2.zip (GEN replicate 2) m) EXP-21-BW5666_NIT-1.zip (NIT replicate 1) n) EXP-22-BY2419_NIT-2.zip (NIT replicate 2) o) EXP-21-BT2898_RIF-1.zip (RIF replicate 1) p) EXP-21-BY1000_RIF-2.zip (RIF replicate 2) q) EXP-21-BW5661_SPT-1.zip (SPT replicate 1) r) EXP-21-BY1019_SPT-2.zip (SPT replicate 2) s) EXP-21-BW5658_TET-1.zip (TET replicate 1) t) EXP-22-BY2421_TET-1.zip (TET replicate 2) 2. 17h exposure to rifampicin (E. coli, S. enterica) These experiments were performed to test the effect of long-term rifampicin exposure on Escherichia coli and Salmonella enterica. a) EXP-21-BT2899.zip (E. coli) b) EXP-21-BY1015.zip (S. enterica) 3. Growth in minimal medium (E. coli) This experiment was performed to test how reducing the cellular growth rate (without antibiotics) affects the cell-to-cell growth heterogeneity. a) EXP-22-BY2420.zip Code The 'codefolder' contains the ImAnalysis pipeline and the UNet used for image analysis. The scripts and parameter files to perform the image analysis are provided within each individual experiment folder.  The 'Data_analysis' folder contains three directories: (i) 'Analysis_scripts', which contains the R scripts used for data analysis and figure generation; (ii) 'Raw_data', which contains the raw data underlying the figures in the paper; and (iii) 'Results', which is the output directory for the figures generated by the analysis scripts. Mon, 12 Dec 2022 00:00:00 GMT https://researchdata.se/sv/catalogue/dataset/doi-10-17044-scilifelab-21517710 https://researchdata.se/sv/catalogue/dataset/doi-10-17044-scilifelab-21517710 Uppsala universitet Gerrit Brandis Jimmy Larsson Johan Elf