Support Facility on Analytics and Robotics
Our focus areas
The sequencing, robotics and bioinformatics wing of the molecular neurobiology group manages the following facilities:
At the Seq-Lab of the molecular neurobiology group we generate high-throughput sequencing libraries required for various sequencers, such as Illumina and Ion Proton sequencers, by using various kits and protocols based on the needs of the projects and our collaborators. We can perform transcriptome sequencing (whole transcriptome, mRNA-Seq, targeted RNA-Seq, small RNA-Seq, scRNAseq), ChIP sequencing, targeted genome sequencing and exome sequencing.
In addition, we have developed a cost-effective 3’-RNA-Seq protocol for Ion Proton and Illumina Sequencers and have ION PGM and ION Proton sequencers in house. Most recently, we have implemented the ddSEQ Single-Cell Isolator as part of the Illumina Bio-Rad Single-Cell Sequencing Solution to our facility.
We also act as a core RNA-Seq service provider for the Glial Heterogeneity Network (SPP1757) for challenging (MACS/ FACS) sorted samples where RNA input is as little as 1-5 ng.
Gene Expression Assays using Real-Time qPCR
In addition, we provide services to set up small- and large-scale quantitative Real-Time PCR (qRT-PCR). qRT-PCR is currently the most sensitive technique available for mRNA detection and quantification. Compared with northern blot analysis and RNase protection assay, qRT-PCR can be used to quantify mRNA levels from much smaller samples and, ultimately, to quantify RNA from a single cell.
The benefit of qRT-PCR is the ability to obtain quantitative results from the sensitive PCR assay. Because qRT-PCR quantitates reaction products for each sample in every PCR cycle, the result is an amazingly broad dynamic range, with no user intervention required. Data analysis, including standard curve generation and copy number calculation, SNP analysis, etc., is performed automatically by the ThermoFischer or Qiagen software connected to our Stepone Plus and Rotorgene PCR machine. In addition, we also perform custom analysis with R (a programming language).
- QRT- SYBR GREEN, TaqMan,
- More than 1000 SYBR-Green assays validated and ready to go.
- SNPs (Using both high resolution melting and AODs from life tech)
- Offers Assay / Primer design
- Step-One Plus (ThermoFischer Scientific)
- Rotorgene (Qiagen)
- LightCycler Nano (Roche)
- ABI-7000 (Life Tech)
Full qRT-PCR service with plates prepared with liquid handler is also available. Please check our Liquid Handling (link to Liquid Handling) page for details.
The bioinformatics sub-group also owns infrastructure that is capable of performing NGS data analysis on demand. We use in-house pipelines that use R Bioconductor Packages and the commercial automated software Partek Flow and perform quality controls, sequence mapping, differential analysis and pathway enrichment analysis.
In addition, we also extend the RNA-Seq Data analysis to protein-protein interaction and data visualisation (such as Circos, Cytoscape, etc.). Moreover, we have a local instance of BLAST for sequence similarity analysis, where we perform EXTAssay data analysis.
We have also established a customized laboratory inventory management system based on Open Freezer. The system tracks information on all reagents within the laboratory, including specific properties of each reagent (i.e. sequences, external identifiers), and on all the physical preparations of these reagents (storage locations, physical characteristics). Complementing this repository are workflow tools, such as primer design and automated feature mapping, making OpenFreezer a valuable tool for the bench scientists.
Our liquid handling service with the Hamilton STAR Plus automation platform provides an accurate and reproducible solution for high-throughput liquid handling of samples. We provide a fully automated system for cell-based assays, including screening projects with luciferase assays or EXTassays as readout technologies. The system can also be used to setup PCR plates in 384/96 plates as well as Rotor-Gene 100 discs.
Our tasks include the following:
- Perform small-scale screening projects: screen small molecule libraries (e.g. NIH collection) with cell-based assays powered by splitSENSOR technology
- Transfer samples from Eppi-Cups to 96/384 well plates or vice versa
- Serial dilutions: create serial dilution plates from original sample plates
- Sample normalisation: normalise samples to the same concentration or volume
- Plate replications: create replicated plates from original plates
- Set up quantitative Real-Time PCR plates (96/384 well plates or 100-disc Rotor-Gene) by using the PCR setup application from Hamilton Robotics
The advantages of Automated Liquid Handling vs. manual pipetting are as follows:
- Frees up hands and time; is more ergonomic
- Avoids human errors, increases reproducibility and accuracy. (Our Hamilton Star Plus system is well maintained with a detailed Standard Operating Protocol that follows Good Laboratory Practices guidelines.)
- Reduces cost: for example, for real-time PCR assays Automated Liquid Handling can run 384 instead of 96 well plates; the smaller reaction volume means lower master mix costs.
We have established a fully automated biobank that is capable of extracting DNA and RNA from various types of samples from large psychiatric study cohorts.
We process and store various patient samples, including:
- Whole blood
Our samples are stored in our fully automated Bios storage system from Hamilton. This automated freezer can accommodate up to 1 million barcoded Matrix tubes.