Project description:This study was designed to construct and quantitatively characterize a synthetic promoter library in Escherichia coli. Promoter variants were assembled into the low-to-medium copy plasmid pSEVA221 to generate the p221-Plib library, in which each promoter was associated with a barcode sequence. The library was introduced into E. coli DH5α, and pooled transformants were cultured under selective conditions. Promoter activities were determined by sequencing barcode abundances from both RNA-derived cDNA and plasmid DNA libraries. The normalized RNA/DNA ratio was used as a quantitative measure of promoter activity, correcting for differences in sequencing depth, plasmid abundance, and clone representation. This dataset provides promoter activity profiles that can facilitate promoter selection and optimization for synthetic biology and metabolic engineering applications.
Project description:Manufacturing adulteration is the major cause of discrepancies between the declared and actual composition of food products. The use of high-throughput sequencing of DNA barcodes is a promising method to identify adulterants, but is not yet widely used in practice. Food pre-processing and differences in GC composition can lead to unequal amplification or complete loss of DNA barcode components, so the results of genomic analysis require an independent confirmation method. Perhaps the most promising way to increase the accuracy of food ingredient identification is to use an orthogonal method based on very different physical principles than DNA sequencing, which involves the analysis of other plant cell components, to verify the results of HTS analysis. In this work, we decided to evaluate the suitability of a multi-omic approach, including coupled DNA barcode HTS analysis and proteomic analysis, to estimate food fraud in herbal beverages. To resolve disputed discordant results obtained during genomic and proteomic investigation of samples, we used traditional botanical morphology method. Among the samples studied, the combined approach revealed two adulterations of Epilobium with Lythrum, which could be dangerous for the unsuspecting consumer.
Project description:HCC827 cells were barcoded using the ClonTracer lentiviral barcode library such that the majority of cells were infected with a single barcode. One million cells were expanded to ~120 million cells and split into 8 HYPERfasks. Two HYPERfasks were grown under DMSO and grown until confluence. In six HYPERfasks cells were grown under a GI90 concentration of one of two different inhibitors, gefitinib and trametinib (3 HYPERfasks each). Cells achieved confluence at 4 and 9 weeks for gefitinib and trametinib respectively. During this time, the medium and inhibitor were replenished weekly and DNA was extracted from the medium to track barcode content from dying cells.
Project description:Random DNA barcode could identified the functional atributes in immunophenotypic HSC fraction. Combined scRNA-seq with tracing random DNA-barcode could identifed specific molecular signature of the theses functional atributes.
Project description:Homo sapiens and Macaca fascicularis neural progenitor cell lines were transduced with a lentiviral MPRA (Massively Parallel Reporter Assay) library. MPRA barcode sequencing and RNA-seq was performed on the extracted RNA. MPRA data was used to compare activity of regulatory sequences across 75 mammalian species with a focus on primates and correlate these activities with the Phenotype of gyrencephaly.
Project description:To investigate immunoediting at the primary tumour, we used DNA barcoding combined with NGS. By stably integrating 4T1 murine cancer cell line with 250000 unique DNA barcodes (1 barcode per cell), we can trace how barcode (and therefore subclonal) diversity changes over time and after treatment with immunotherapy.
Project description:To investigate immunoediting at the primary tumour, we used DNA barcoding combined with NGS. By stably integrating 4T1 murine cancer cell line with 5000 unique DNA barcodes (1 barcode per cell), we can trace how barcode (and therefore subclonal) diversity changes over time and after treatment with immunotherapy.
Project description:To investigate immunoediting at the primary tumour, we used DNA barcoding combined with NGS. By stably integrating 4T1 murine cancer cell line with 5000 unique DNA barcodes (1 barcode per cell), we can trace how barcode (and therefore subclonal) diversity changes over time and after treatment with immunotherapy.
