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en:aree:ngs:start [2018/09/05 15:35] Gianluca Frustagli |
en:aree:ngs:start [2024/07/10 17:21] (current) Gianluca Frustagli Updated reference to Bio-Fab collaboration. |
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| **Area** | **Area** | ||
| - | ====== Sequencing ====== | + | ====== Next Generation Sequencing (NGS) ====== |
| - | \\ | + | <WRAP tabs> |
| + | * [[en:aree:ngs:start|Mission]] | ||
| + | * [[en:aree:ngs:strumenti|Instrumentation]] | ||
| + | * [[en:aree:ngs:servizi|Services]] | ||
| + | * [[en:aree:ngs:eventi|Events]] | ||
| + | * [[en:aree:ngs:richiesta|Requests]] | ||
| + | * [[en:aree:ngs:chi_siamo|Staff]] | ||
| + | </WRAP> | ||
| - | The ISS sequencing service is equipped with the <wrap em>Ion GeneStudio S5 System</wrap>, a next-generation sequencing (NGS) system based on semiconductor technology (Ion S5 chip) that enables simple and fast //multi-targeted// sequencing workflows with high accuracy at reduced costs. | + | {{ :aree:ngs:lab_ngs.jpeg |}} |
| - | Whenever a single nucleotide is incorporated during DNA polymerization, a hydrogen ion is released: the resulting pH variation is detected by the instrument within each CHIP well. The nucleotide incorporation is associated to each pH variation and the chemical signal is then converted into digital signal. Since the growing complementary DNA strand is flooded with a single species of nucleotide at a time, a signal is detectable only when a nucleotide is successfully incorporated. | + | \\ |
| - | The Ion GeneStudio S5 System enables multiplexing of up to 96 fragment libraries on a single sequencing chip thank to the use of specific molecular //barcodes// for sample-labelling. | + | The NGS area aims to offer cutting-edge sequencing technologies and high-quality data to researchers from the ISS and external institutions, both academic and private. |
| - | For DNA analysis, the required starting material is about 10-100 ng (at 10 ng/µl). | + | The expert staff of the NGS area accompanies the researcher in all phases: from the experimental design to the final data for applications such as microbial sequencing (SWGS, both re-sequencing and de novo, 16S, RNAseq), targeted DNA and RNA based on Ampliseq technology (human and mouse transcriptome, Sars-CoV-2 panel, other specific panels), exome, total RNA, microRNA, LncRNA, circulating DNA (ctDNA), amplicon sequencing. |
| - | + | ||
| - | The availability of 4 chip sizes (Ion chip 510, 520, 530 and 540) fits with many different applications and throughput needs and allows to achieve from 2–80 million reads per run. | + | |
| + | The NGS facility collaborates with researchers, both internal to the ISS and external, for the implementation of new applications. The facility also supports researchers in preparing funding applications for projects involving Next Generation Sequencing and single cell OMICs. | ||
| \\ | \\ | ||
| - | <WRAP centeralign> | + | <WRAP center round info 65%> |
| - | + | {{:aree:in_collaborazione:biofab_research:biofab_research.png?200}} | |
| - | {{aree:ngs:strumento-v2.jpeg?0x300|The instrument}} {{aree:ngs:chip-v2.jpeg?0x300|The semiconductor chip}} | + | |
| - | + | ||
| - | <wrap lo>On the left: the instrument -- on the right: the semiconductor chip</wrap> | + | |
| - | + | ||
| - | \\ \\ | + | |
| - | + | ||
| - | {{aree:ngs:funzionamento.png|NGS: mechanism of action}} | + | |
| - | + | ||
| - | <wrap lo>Il principio di funzionamento</wrap> | + | |
| + | Since 2018-09-21 the ISS has established a scientific collaboration with **[[https://www.biofabresearch.it|Bio-Fab Research]]**. The aim is to enhance the ISS NGS FAST facility... [[en:aree:in_collaborazione:biofab_research:|[read more]]] | ||
| </WRAP> | </WRAP> | ||
| \\ | \\ | ||
| - | ==== Applications ==== | ||
| - | |||
| - | Ion GeneStudio S5 technology is mainly indicated for the following applications: | ||
| - | * **Microbial sequencing** (DNA, RNA , //also de novo//); | ||
| - | * **whole exome and transcriptome**; | ||
| - | * **Targeted DNA and RNA** sequencing based on the Ampliseq technology, | ||
| - | * **Small RNA and miRNA** sequencing; | ||
| - | |||
| - | \\ | ||
| ==== To ask for the NGS service: ==== | ==== To ask for the NGS service: ==== | ||
| Line 54: | Line 43: | ||
| \\ | \\ | ||
| - | > Contact: [[fiorella.ciaffoni@iss.it|Fiorella Ciaffoni]] | + | > Contact: [[manuela.marra@iss.it|Manuela Marra]] |
| - | > ☎ **+39 06 4990 3074/3051** | + | > ☎ **+39 06 4990 3051** |
| - | > FIXME **To be revised.**\\ //(remove this paragraph once finished)// | + | /* > FIXME **To be revised.**\\ //(remove this paragraph once finished)// */ |
