<\/p>\n
- \n
- Quality Control<\/strong><\/li>\n<\/ul>\n
Quality control is essential to ensure the integrity and reliability of samples and sequencing procedures<\/strong>. To achieve this, we use two complementary<\/strong> yet distinct instruments that provide peak and smear analysis<\/strong> of genetic material: Fragment Analyzer<\/strong> and TapeStation<\/strong>.<\/p>\n
<\/p>\n
Fragment Analyzer
\n<\/strong><\/strong><\/h5>\nThe Fragment Analyzer uses capillary electrophoresis<\/strong>, offering high precision and sensitivity<\/strong>, even with low-input samples<\/strong>. This instrument is ideal for projects analyzing 6 to 11 samples or more<\/strong>, as it operates by lane. We offer high-sensitivity kits<\/strong>, ensuring accurate assessment of nucleic acid quality:<\/p>\n
- \n
- NGS Fragment Kit (1-6000bp)<\/li>\n
- HS RNA Kit (15NT)<\/li>\n<\/ul>\n
<\/p>\n
TapeStation<\/h5>\n
The TapeStation is based on microfluidic electrophoresis<\/strong> and processes each sample individually<\/strong>, making it more flexible for varying sample numbers. We provide a range of kits tailored to different sample types, fragment sizes, and concentrations<\/strong>, including:<\/p>\n
- \n
- D5000 & D5000 HS<\/li>\n
- D1000 & D1000 HS<\/li>\n
- Genomic DNA<\/li>\n
- RNA & RNA HS<\/li>\n<\/ul>\n
These QC tools help guarantee that only high-quality samples proceed to sequencing, maximizing the success and reliability of downstream analyses.<\/p>\n
<\/p>\n
- \n
- Library Preparation<\/strong><\/li>\n<\/ul>\n
Our facility offers library preparation services for multiple sequencing platforms, including Illumina, MGI, and Nanopore<\/strong>, ensuring flexibility for diverse research needs.<\/p>\n
<\/p>\n
Illumina Library Preparation<\/h5>\n
We provide a range of protocols tailored to different applications:<\/p>\n
- \n
- Amplicon Sequencing\/ Metabarcoding \u2013<\/strong> We support 16S, 18S, and ITS sequencing for microbial community profiling. Our standard protocol targets specific conserved gene regions, but researchers can opt for customized protocols to meet specific experimental requirements.<\/li>\n
- Whole Genome Sequencing (WGS) \u2013<\/strong> For DNA library preparation, we utilize the Nextera XT protocol, optimized for high-throughput sequencing.<\/li>\n
- Bulk RNA Sequencing \u2013<\/strong> We prepare RNA libraries from total RNA or cells using the Smart-seq2 protocol, enabling comprehensive gene expression analysis. Additionally, we offer ribodepletion using the Zymo-Seq RiboFree Total RNA Library Kit, which removes ribosomal RNA to improve the detection of low-abundance transcripts.<\/li>\n
- Single-Cell RNA Sequencing \u2013<\/strong> For high-resolution transcriptomics, we use 10x Genomics technology, allowing the analysis of thousands of individual cells in a single experiment.<\/li>\n<\/ul>\n
<\/p>\n
Library Preparation for MGI Sequencing<\/h5>\n
MGI sequencing is an advanced technology that generates DNA Nanoballs (DNBs)<\/strong> from circularized DNA molecules. These DNBs<\/strong> are multiple copies of a single fragment arranged in a compact ball, which adheres to a patterned flow cell<\/strong>. This method significantly reduces PCR bias<\/strong>, as no amplification occurs inside the sequencer, leading to more accurate and uniform sequencing results.<\/p>\n
Our facility provides library preparation for MGI sequencing, supporting various applications:<\/p>\n
DNA Library Preparation:<\/strong><\/p>\n
- \n
- Free-PCR Library Construction \u2013 Ideal for applications where minimal amplification is preferred.<\/li>\n
- Fast Library Construction \u2013 A rapid and efficient method for DNA library preparation.<\/li>\n<\/ul>\n
RNA Library Preparation:<\/strong><\/p>\n
- \n
- MGIEasy Fast RNA \u2013 Designed for fast and efficient RNA sequencing.<\/li>\n<\/ul>\n
Illumina-to-MGI Library Conversion:<\/strong><\/p>\n
- \n
- We offer a library conversion service, enabling researchers to use pre-existing Illumina libraries for MGI sequencing.<\/li>\n<\/ul>\n
<\/p>\n
Nanopore<\/h5>\n
Nanopore Sequencing is a cutting-edge technology that enables real-time, long-read sequencing<\/strong> by passing DNA or RNA molecules through biological nanopores<\/strong>. As nucleotides move through the pore, changes in electrical current are detected, allowing for direct base calling without the need for amplification. This method offers unprecedented read lengths<\/strong>, the ability to detect base modifications<\/strong>, and the flexibility to sequence in real-time<\/strong> on portable or high-throughput devices. Nanopore sequencing is ideal for whole genome sequencing, transcriptomics, epigenetics, and rapid pathogen detection<\/strong>, providing a powerful tool for diverse genomics applications.<\/p>\n","gallery":false},{"title":"Technology and Equipment","description":"
Quality Control & Fragment Analysis<\/h3>\n
<\/p>\n
![\"\"](\"https:\/\/gimm.pt\/wp-content\/uploads\/2024\/07\/Picture1_Genomics.png\")
<\/p>\n- \n
- Fragment Analyzer (Agilent) \u2013<\/strong> An automated capillary electrophoresis system.<\/li>\n
- TapeStation 4200 (Agilent) \u2013<\/strong> A fluorescence-based microfluidic electrophoresis system.<\/li>\n<\/ul>\n
<\/p>\n
Sequencing Platforms<\/h3>\n
<\/p>\n
![\"\"](\"https:\/\/gimm.pt\/wp-content\/uploads\/2024\/07\/Picture2_Genomics.png\")
<\/p>\n- \n
- NextSeq 2000 (Illumina) \u2013<\/strong> A versatile high-throughput sequencer offering four different capacities (100M, 400M, 1200M, and 1800M reads) with read lengths ranging from SE50 to PE300 (300+300).<\/li>\n
- MiSeq (Illumina) \u2013<\/strong> The ideal sequencer for amplicon sequencing (16S\/18S, ITS) and small-scale projects, offering longer read lengths of up to 600 cycles (300+300).<\/li>\n
- G400 (MGI) \u2013<\/strong> A flexible sequencer supporting multiple read lengths (SE50 to PE300) with an output range of 55 Gb to 1440 Gb per run.<\/li>\n
- PromethION (Nanopore P2S) \u2013<\/strong> A compact, high-yield long-read sequencer, capable of generating up to 580 Gb per run and up to 2 Mb per individual read, making it ideal for whole genome sequencing, epigenetics, and transcriptomics.<\/li>\n
- MinION (Nanopore) \u2013<\/strong> A portable, real-time long-read sequencer, suitable for smaller-scale projects requiring rapid and cost-effective sequencing.<\/li>\n<\/ul>\n
<\/p>\n
Single-Cell & Spatial Genomics<\/h3>\n
<\/p>\n
![\"\"](\"https:\/\/gimm.pt\/wp-content\/uploads\/2024\/07\/Picture3_Genomics.png\")
<\/p>\n- \n
- Chromium X (10x Genomics) \u2013<\/strong> A highly flexible single-cell system, capable of handling low, medium, and high-throughput single-cell assays, immune profiling, and fixed RNA analysis (human and mouse only).<\/li>\n
- The unit offers 10X Genomics Visium Spatial Transcriptomics service and STOmics Stereo-Seq with the Histopathology and Bioimaging Facilities. This allows for transcriptome-wide mapping of genes expression onto tissue sections, with concomitant H&E or IF staining. The option to process both FFPE slides or Fresh frozen tissues is available.<\/li>\n<\/ul>\n
<\/p>\n
Automation for High-Throughput Processing<\/h3>\n
<\/p>\n
![\"\"](\"https:\/\/gimm.pt\/wp-content\/uploads\/2024\/07\/Picture4_Genomics.png\")
<\/p>\n- \n
- Biomek i7 (Beckman) \u2013<\/strong> A high-performance liquid handling workstation designed for automating library preparation and sample processing. With up to 45 deck positions, a dual pipetting system, and an enclosed workspace, it enhances reproducibility, accuracy, and efficiency for large-scale experiments.<\/li>\n<\/ul>\n","gallery":false},{"title":"How to use the service","description":"
Our facility provides customized solutions<\/strong> to meet the unique needs of each project. Contact us to discuss how our advanced technologies<\/strong> can support your research.<\/p>\n
<\/p>\n
Getting started with our services is simple! Follow these steps to create an account and request a quote:<\/p><\/blockquote>\n
- The unit offers 10X Genomics Visium Spatial Transcriptomics service and STOmics Stereo-Seq with the Histopathology and Bioimaging Facilities. This allows for transcriptome-wide mapping of genes expression onto tissue sections, with concomitant H&E or IF staining. The option to process both FFPE slides or Fresh frozen tissues is available.<\/li>\n<\/ul>\n
- MiSeq (Illumina) \u2013<\/strong> The ideal sequencer for amplicon sequencing (16S\/18S, ITS) and small-scale projects, offering longer read lengths of up to 600 cycles (300+300).<\/li>\n
- TapeStation 4200 (Agilent) \u2013<\/strong> A fluorescence-based microfluidic electrophoresis system.<\/li>\n<\/ul>\n
- Fragment Analyzer (Agilent) \u2013<\/strong> An automated capillary electrophoresis system.<\/li>\n
- We offer a library conversion service, enabling researchers to use pre-existing Illumina libraries for MGI sequencing.<\/li>\n<\/ul>\n
- MGIEasy Fast RNA \u2013 Designed for fast and efficient RNA sequencing.<\/li>\n<\/ul>\n
- Whole Genome Sequencing (WGS) \u2013<\/strong> For DNA library preparation, we utilize the Nextera XT protocol, optimized for high-throughput sequencing.<\/li>\n
- Amplicon Sequencing\/ Metabarcoding \u2013<\/strong> We support 16S, 18S, and ITS sequencing for microbial community profiling. Our standard protocol targets specific conserved gene regions, but researchers can opt for customized protocols to meet specific experimental requirements.<\/li>\n
- Library Preparation<\/strong><\/li>\n<\/ul>\n