EC0900 Lot 1 - Short Read Genomic Sequencing

Tender description

You are invited by The University of Edinburgh (UoE) to tender for a position on a lotted framework covering a wide range of Sequencing and Genotyping services. The UoE have internally available resources and this framework is designed to support these resources. Our end-users will be encouraged to approach our internal resources first and foremost but if capability, capacity or cost isn't suitable, then successful suppliers on the framework will be able to compete for this business. This procurement process aims to establish a family of Framework Agreements (all under the UoE procurement reference of EC0900) which shall be used to service future sequencing/genotyping projects, subject to their own project specific needs. Open Tender - creation of a framework. The aim is to establish a family of frameworks to provide sequencing/genotyping services support to our internally available resources i.e. Edinburgh Genomics, the Genome Foundry, etc. Lot 1: Lot 1 - Short Read Genomic Sequencing & Analysis Paired end library sequencing Long mate pair library sequencing Linked read sequencing Genome Sequence imputation Including data transfer QC of sequence data - specific to the lot Including Library Prep (and sample QC) - specific to the lot Bioinformatic Services - Data Analysis, Interpretation & Reporting of sequencing services - specific to the lot Lot 2: Lot 2 - Long Read Genomic Sequencing & Analysis Pacific Biosciences (PacBio) Sequencing Oxford Nanopore Technology (ONT/Nanopore) sequencing VASA-Seq Including data transfer QC of sequence data - specific to the lot Including Library Prep (and sample QC) - specific to the lot Bioinformatic Services - Data Analysis, Interpretation & Reporting of sequencing services - specific to the lot Lot 3: Lot 3 - Transcriptome Sequencing & Analysis RNA-Sequencing (mRNA and total RNA sequencing) full length transcript or cDNA sequencing Small RNA Sequencing Nanostring Microarray services Direct RNA sequencing (Oxford Nanopore) Including data transfer QC of sequence data - specific to the lot Including Library Prep (and sample QC) - specific to the lot Bioinformatic Services - Data Analysis, Interpretation & Reporting of sequencing services - specific to the lot Lot 4: Lot 4 - Targeted Sequencing & Analysis Exome Sequencing Targeted / Gene Sequencing Custom sequence capture Including data transfer QC of sequence data - specific to the lot Including Library Prep (and sample QC) - specific to the lot Bioinformatic Services - Data Analysis, Interpretation & Reporting of sequencing services - specific to the lot Lot 5: Lot 5 - Microbial Sequencing & Analysis Whole Genome PacBio Sequencing (for microbial) Whole Genome Nanopore Sequencing (for microbial) Whole Genome Short Read Sequencing (for microbial) 16s Microbial Sequencing Including data transfer QC of sequence data - specific to the lot Including Library Prep (and sample QC) - specific to the lot Bioinformatic Services - Data Analysis, Interpretation & Reporting of sequencing services - specific to the lot Lot 6: Lot 6 - Single Cell Sequencing & Analysis Single Cell Isolation and Sequencing Single Nuclei Isolation and Sequencing Single cell ATAC-Seq Including data transfer QC of sequence data - specific to the lot Including Library Prep (and sample QC) - specific to the lot Bioinformatic Services - Data Analysis, Interpretation & Reporting of sequencing services - specific to the lot Lot 7: Lot 7 - Other Genomic Methods & Analysis Methylation Sequencing (reduced representation or whole genome bisulphite sequencing) ATAC-Seq Library Preparation ChiP-Seq Library Preparation HiC library preparation / sequencing RIP-Seq Ribo-Seq Including data transfer QC of sequence data - specific to the lot Including Library Prep (and sample QC) - specific to the lot Bioinformatic Services - Data Analysis, Interpretation & Reporting of sequencing services - specific to the lot Lot 8: Lot 8 - Optical Mapping Optical Mapping Including data transfer QC of sequence data - specific to the lot Including Library Prep (and sample QC) - specific to the lot Bioinformatic Services - Data Analysis, Interpretation & Reporting of sequencing services - specific to the lot Lot 9: Lot 9 - Sanger Sequencing / Genotyping Sanger sequencing / genotyping Plasmid DNA extraction Lot 10: Lot 10 - Array-based genotyping Genotyping of Single Nucleotide Polymorphism (SNP) Array-based genotyping Include all-inclusive genotyping services - specific to the lot Lot 11: Lot 11 - Other Genotyping services Genotyping of simple sequence repeat (SSR) Genotyping by Microsatellite Genotyping of low number SNPs Include all-inclusive genotyping services - specific to the lot - specific to the lot Lot 12: Lot 12 - Genotyping of transgenic animals Genotyping of transgenic animals Genetic background characterisation 1-7 genes per animal, with up to 6 different alleles detectable for each gene a panel of genetic markers that can distinguish between the common lab strains of mouse and rat evenly spaced through the genome Lot 13: Lot 13 - DNA/RNA Extraction whole blood Saliva FTA paper Buccal swabs Mammalian cell lines/primary cells (cell pellets) Plant and animal tissue FFPE tissue Bacteria Lot 1: Lot 1 - Short Read Genomic Sequencing & Analysis Paired end library sequencing Long mate pair library sequencing Linked read sequencing Genome Sequence imputation Including data transfer QC of sequence data - specific to the lot Including Library Prep (and sample QC) - specific to the lot Bioinformatic Services - Data Analysis, Interpretation & Reporting of sequencing services - specific to the lot Lot 2: Lot 2 - Long Read Genomic Sequencing & Analysis Pacific Biosciences (PacBio) Sequencing Oxford Nanopore Technology (ONT/Nanopore) sequencing VASA-Seq Including data transfer QC of sequence data - specific to the lot Including Library Prep (and sample QC) - specific to the lot Bioinformatic Services - Data Analysis, Interpretation & Reporting of sequencing services - specific to the lot Lot 3: Lot 3 - Transcriptome Sequencing & Analysis RNA-Sequencing (mRNA and total RNA sequencing) full length transcript or cDNA sequencing Small RNA Sequencing Nanostring Microarray services Direct RNA sequencing (Oxford Nanopore) Including data transfer QC of sequence data - specific to the lot Including Library Prep (and sample QC) - specific to the lot Bioinformatic Services - Data Analysis, Interpretation & Reporting of sequencing services - specific to the lot Lot 4: Lot 4 - Targeted Sequencing & Analysis Exome Sequencing Targeted / Gene Sequencing Custom sequence capture Including data transfer QC of sequence data - specific to the lot Including Library Prep (and sample QC) - specific to the lot Bioinformatic Services - Data Analysis, Interpretation & Reporting of sequencing services - specific to the lot Lot 5: Lot 5 - Microbial Sequencing & Analysis Whole Genome PacBio Sequencing (for microbial) Whole Genome Nanopore Sequencing (for microbial) Whole Genome Short Read Sequencing (for microbial) 16s Microbial Sequencing Including data transfer QC of sequence data - specific to the lot Including Library Prep (and sample QC) - specific to the lot Bioinformatic Services - Data Analysis, Interpretation & Reporting of sequencing services - specific to the lot Lot 6: Lot 6 - Single Cell Sequencing & Analysis Single Cell Isolation and Sequencing Single Nuclei Isolation and Sequencing Single cell ATAC-Seq Including data transfer QC of sequence data - specific to the lot Including Library Prep (and sample QC) - specific to the lot Bioinformatic Services - Data Analysis, Interpretation & Reporting of sequencing services - specific to the lot Lot 7: Lot 7 - Other Genomic Methods & Analysis Methylation Sequencing (reduced representation or whole genome bisulphite sequencing) ATAC-Seq Library Preparation ChiP-Seq Library Preparation HiC library preparation / sequencing RIP-Seq Ribo-Seq Including data transfer QC of sequence data - specific to the lot Including Library Prep (and sample QC) - specific to the lot Bioinformatic Services - Data Analysis, Interpretation & Reporting of sequencing services - specific to the lot Lot 8: Lot 8 - Optical Mapping Optical Mapping Including data transfer QC of sequence data - specific to the lot Including Library Prep (and sample QC) - specific to the lot Bioinformatic Services - Data Analysis, Interpretation & Reporting of sequencing services - specific to the lot Lot 9: Lot 9 - Sanger Sequencing / Genotyping Sanger sequencing / genotyping Plasmid DNA extraction Lot 10: Lot 10 - Array-based genotyping Genotyping of Single Nucleotide Polymorphism (SNP) Array-based genotyping Include all-inclusive genotyping services - specific to the lot Lot 11: Lot 11 - Other Genotyping services Genotyping of simple sequence repeat (SSR) Genotyping by Microsatellite Genotyping of low number SNPs Include all-inclusive genotyping services - specific to the lot - specific to the lot Lot 12: Lot 12 - Genotyping of transgenic animals Genotyping of transgenic animals Genetic background characterisation 1-7 genes per animal, with up to 6 different alleles detectable for each gene a panel of genetic markers that can distinguish between the common lab strains of mouse and rat evenly spaced through the genome Lot 13: Lot 13 - DNA/RNA Extraction whole blood Saliva FTA paper Buccal swabs Mammalian cell lines/primary cells (cell pellets) Plant and animal tissue FFPE tissue Bacteria