Project description:Several template DNA molecules with random base molecular barcodes were amplified and sequenced, and the efficacy of the random base barcode for digital counting was shown.
Project description:Combinatorial promoter expression level estimation via cell sorting The purpose of this experiment was to determine the expression level of a library of synthetic promoters. The promoters were cloned in front of a GFP reporter and the resulting library transformed into yeast, sorted by FACS into six fluorescence bins, and the contents of the bins sequenced to determine the distribution of each promoter among each fluorescence bin. This was then used to calculate an expression level for each promoter with enough data. The promoters were sorted into six bins and these, along with the unsorted library were barcoded and sequenced on a single lane of an Illumina HiSeq. The following Series supplementary files are provided: allPromoters.fsa.txt: the sequences of the promoters corresponding to the names in allPromoters.txt, not actually fasta format. Promoter sequence starts at pos 155 (0 indexed). allPromoters.txt: the names of all the promoters, corresponding to the sequences in allPromoters.fsa.txt barcodes.txt: the sequncing barcodes, corresponding to read2 from the sequencing files.
Project description:Previous methods to systematically characterize sequence-intrinsic activity of promoters have been limited by relatively low throughput and the length of sequences that could be tested. Here we present Survey of Regulatory Elements (SuRE), a method to assay more than 10^8 DNA fragments, each 0.2-2kb in size, for their ability to drive transcription autonomously. In SuRE, a plasmid library is constructed of random genomic fragments upstream of a 20bp barcode and decoded by paired-end sequencing. This library is then transfected into cells and transcribed barcodes are quantified in the RNA by high throughput sequencing. When applied to the human genome, we achieved a 55-fold genome coverage, allowing us to map autonomous promoter activity genome-wide. By computational modeling we delineated subregions within promoters that are relevant for their activity. For instance, we show that antisense promoter transcription is generally dependent on the sense core promoter sequences, and that most enhancers and several families of repetitive elements act as autonomous transcription initiation sites.
Project description:20 random DNA barcodes were designed in silico and transfected into PC3 cells. Barcodes were sequenced using Illumina-Miseq technology to find the sequence and their respective copy numbers. Current file contains the raw data of these DNA barcodes in fastq format
Project description:20 random DNA barcodes were designed in silico and transfected into PC3 cells. Barcodes were sequenced using Illumina-Miseq technology to find the sequence and their respective copy numbers. Current file contains the raw data of these DNA barcodes in fastq format Validating an algorithm called SRiD that generates random DNA barcodes that do not match a genome of interest, in this case human genome. 20 DNA barcodes were used for this validation.
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.
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.