The Genomics, Sandbox unit, 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), NovaSeqX Plus Iillumina sequencing, 10x genomics single cell multiomics ans spatial transcriptomics, and bulk ATAC-seq.
Coming soon - We will soon implement the Vega long read sequencing of PacBio https://www.pacb.com/vega/.
Bulk MARS-seq is a high-throughput, low-input 3’-mRNA-seq method. The protocol involves barcoding of samples by reverse transcription using an oligo dT primer, pooling of samples, and subsequent molecular reactions for linear amplification and preparation for Illumina sequencing. For references, see (Jaitin et al., Science, 2014; Keren-Shaul et al., Nature Protocols, 2019). The protocol is designed for preparation of 3' RNA sequencing libraries from 1-50 ng of total RNA.
The Mars-seq protocol will be taught in a 3-day 'hands-on' workshop. 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.
The newest high throughput Illumina sequencing platform NovaSeq X Plus. It presents XLEAP-SBS chemistry that delivers the highest level of data accuracy and performance, with increased stability.
Sequencing ouptut is 1.5B, 10B or 25B reads per kit at 100, 200 or 300 cycles read length.
The instrument is locdated at the INCPM genomics unit (solar tower) and is open for sandbox independent usage.
AVITI is a benchtop sequencing instrument (by Element Biosciences) with reimagined core technology to deliver flexibility and affordability while setting the standard for data quality.
Sequencing output is up to 1B reads per run at 2*75 cycles read length. Additional kits are available upon request.
The 10x Genomics tehcnologies offers high throuhgput single cell multiomics using GEM-X microfluidics technology.
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
The bulk ATAC-seq is based on the OMNI-ATAC protocol (Grandi et al., Nature Protocols 2022). ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) (Buenrostro et al, Nature Methods 2013) uses Tn5, a hyperactive transposase loaded with sequencing adapters, to map chromatin-accessible regions (nucleosome depleted), often containing regions of active genes and their promoters and enhancers. ATAC-seq is commonly used with other methods to infer regulatory regions in the genome.
The OMNI-ATAC is a newer version of the ATAC-seq protocol that uses a combination of three detergents to lyse the cells and gives more robust results with a lower background. The recommended input is 50,000 cells, either freshly isolated or cryo-preserved.
The Agilent 2200 TapeStation system offers an automated electrophoresis platform for quality control of DNA and RNA samples.
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.
The Covaris 220X is an ultrasonicator that performs shearing of DNA fragements.