The Advanced sequencing technologies, Sandbox, serves as an advanced genomics technological laboratory that allows Weizmann's scientists access to state-of-the-art genomic technologies and protocols from advanced labs in the institute. The unit introduces the technologies by the form of 'hands-on' workshops, following which the user can independently use the Sandbox equipment and consumables. Currently, the genomic technologies available in the Sandbox are: Mars-seq (preparation of libraries for RNA-seq), Illumina Nextseq sequencing, 10x genomics (single cell RNA-seq) and PacBio (long read sequencing).
Mars-seq – a protocol for preparation of libraries for RNA-seq
The Mars-seq workshop is a 3-day 'hands-on' exercise of the latest development of the 'bulk MARS-seq' protocol developed in Ido Amit lab. The protocol is designed for preparation of 3' RNA sequencing libraries from 1-50 ng of total RNA. In the workshop, each participant will learn to generate sequence-ready libraries starting from standard RNA samples using Sandbox equipment and consumables. Following the basic workshop training, the user will be able to independently use Sandbox equipment and consumables for library preparation of his/her own samples. Up to 96 libraries can be prepared simultaneously which can be sequenced in the unit's Nextseq desktop sequencer. Workshops are free of charge and limited to 3 participants. Workshops are open for Weizmann students and scientists only, and take place periodically on an approximately once a month schedule. Only workshop graduates will be able to use the sandbox facility
Short read Sequencing - Nextseq 550, Illumina
The unit has Nextsq 550 , that provide the flexible power and simplicity for transcriptome, exome and whole genome sequencing in a single run.
Single cell RNA-seq – Chromium, 10x Genomics
The 10x Genomics Chromium is based on GemCode technology and allows high throughput single cell 3' transcriptomics, genome or exome sequencing.
Spatial transcriptomics - Visium, 10x Genomics
Spatial transcriptomics is assigning cell types to their location in the tissue, hence enabling to elucidate cell heterogeneity and define cell types while also retaining spatial information. The unit is using both the Visium fresh frozen and Visium FFPE kits (10X Genomics).
For more information visit https://www.10xgenomics.com/products/spatial-gene-expression
Long read sequencing – Sequel, PacBio
The PacBio Sequel sequencing system is built on Single molecule, Real-Time (SMRT) Sequencing and provides high consensus accuracy, uniform coverage and long read sequencing.
Microarrays (Affymetrix and Agilent)
Microarray technology is a simple but robust method to screen thousands of probes at once. Microarrays are mostly used to monitor differential expression by placing thousands of gene fragments on a solid surface (such as glass), and querying them with labeled RNA which was extracted from cells/tissues that need to be compared. However, microarrays can be used for other purposes as well, such as SNP scoring, CGH, Transcript mapping, micro-RNA, protein interactions, and more. The goal of the microarray core facility is to provide complete microarray solutions to the research community. The unit supports multiple applications and has expertise in a wide variety of microarray-based technologies and techniques including Affymetrix, Agilent and custum spotted arrays.
The Agilent 2200 TapeStation system offers automated sample processing for quick and reliable sample quality control (RNA or DNA) within any Next Generation Sequencing (NGS), microarray (aCGH) or quantitative PCR (qPCR) workflow.
The FluidigmBioMark System includes the optical, thermal cycling, and software components necessary to perform real-time quantitative PCR (qPCR) analysis on Dynamic Array IFCs. The BioMark System provides orders of magnitude higher throughput for real-time qPCR compared to conventional platforms due to its Dynamic Array IFCs - nanofluidic chips that contain fluidic networks that automatically combine sets of samples with sets of assays. This innovative solution for real-time qPCR provides reaction densities far beyond what is possible with microtiter plates and significantly reduces the number of liquid-handling steps, the volume per reaction and the cost. The system allows you to perform analysis of Gene Expression, SNP Genotyping, Digital PCR and Single-cell Gene Expression and also perform Targeted enrichment for High-throughput Sequencing.
C1 Single-Cell Auto Prep system
The C1 Single-Cell Auto Prep System is the world's first commercially available, automated single-cell isolation and preparation system for genomic analysis. The C1 System provides an easy and highly reproducible gene expression workflow to process 96 single cells across 96 mRNA targets. This new system enables you to rapidly explore unique attributes of individual cells without the technical variability of a standard gene expression workflow. The C1 System enables you to study cell differentiation, measure individual cell responses to specific stimuli, verify critical disease biomarkers, validate RNAi knockdown, and conduct candidate drug screens. With an optimized protocol, pre-formulated reagent kit, and disposable IFCs, you can achieve single-cell accuracy with "load and go" productivity.
The platform features the ability for targeted size selection of DNA fragments (90bp-50kb) with minimal effort for the purpose of Next-Generation Sequencing. Target sizes or ranges of sizes are entered in software, and fractions are collected in buffer. Up to 5 samples per gel cassette may be run, with no possibility of cross contamination. The Blue Pippin can also use SDS-agarose gel cassettes to collect targeted protein sizes from complex samples for biomarker or protein modification studies.