Essential Consumables for Spatial Biology:

Disposable steel blades (for microtomes) or carbide knives (for cryostats) are needed to repeatedly slice tissues. Ensuring sharp, high-quality blades is key to getting intact sections without tears or folds. Brushes, forceps, and spatulas are also used to handle delicate sections and position them on slides.

Standard microscope slides often require a coating (e.g. poly-L-lysine or charged slides) to help tissue sections adhere, especially for FFPE sections that will undergo washes. Having slides designed for tissue adhesion prevents sections from detaching during processing. Many labs use “plus” slides or silane-coated slides for this purpose – these are common lab consumables available through Avantor in bulk packs.

A unique consumable for spatial transcriptomics workflows is the barcoded slide. Unlike plain glass slides, these specialized slide kits have an array of spatially encoded oligonucleotides printed on their surface. When a tissue section is placed on such a slide, any mRNA captured from that tissue inherits a positional barcode from the slide. This technology, first introduced by Ståhl et al. (2016) and commercialized in platforms like 10x Genomics Visium, enables mapping of gene expression to coordinates on the tissue. In practice, these slides come with pre-spotted capture probes (often poly(dT) to bind mRNA) in a grid pattern. Each spot on the slide has a unique barcode, so transcripts from cells in one location are tagged differently than those just 100 microns away. If your lab is performing spatial transcriptomics, obtaining the appropriate barcoded slide kit is mandatory. Avantor can help source these specialized consumables (often sold as part of spatial transcriptomics kits) and ensure you have the correct format for your platform – an important consideration, since slides are usually vendor-specific. For labs using emerging DIY methods (like printing your own oligo arrays), Avantor also offers microarray slides and reagents to create custom barcoded surfaces.

Maintaining sample identity and integrity is crucial. Labs should have durable barcode labels for slides (especially if processing many samples) and slide storage boxes or humidity-controlled chambers to hold sections before use. Keeping sections at proper temperature (e.g. in a 4°C fridge for short-term, or -80°C if long-term storage of slides with tissue) often requires sealed slide mailers and desiccants to avoid moisture.

If you are using a sequencing-based platform (like the barcoded slides mentioned earlier), the tissue on the slide will be subjected to a series of enzymatic reagents that capture and tag RNA. Permeabilization buffers are applied to the tissue to lyse cells just enough to release mRNAs onto the slide. Then a reverse transcription kit is used on-slide: it contains enzymes (reverse transcriptase), primers (often the barcoded oligo on the slide acts as a primer), dNTPs, etc. This process creates cDNA from the captured mRNA, incorporating spatial barcodes and unique molecular identifiers (UMIs). After first-strand synthesis, additional reagents are used to denature and collect the cDNA, which then goes into a library prep kit. All these reagents – permeabilization enzymes, RT mix, amplification and library prep kits – are specialized consumables. They often come bundled in spatial transcriptomics kits provided by platform manufacturers. Avantor helps labs by offering a variety of these kits and related molecular biology reagents, so you can obtain your reverse transcriptase, amplification enzymes, and indexing primers through a single source. Even if you’re assembling a custom workflow, you’ll need high-quality PCR enzymes, purification beads, and indexing adapters as consumables for this labeling process.

An alternative approach is using hybridization panels to detect a predefined set of genes in situ. Techniques like RNAscope (RNA in situ hybridization) or multiplexed FISH methods fall in this category. In these workflows, you will use a kit of target-specific probes that hybridize directly to mRNA within the tissue section. For example, the MERFISH technique uses hundreds of fluorescent probes to bind transcripts, and then reads them out via microscopy. Vizgen’s MERSCOPE platform provides gene panels and hybridization buffers as consumables, enabling detection of up to 500 genes with subcellular resolution . Essential consumables here include the probe set (often a mixture of DNA oligonucleotides designed for your genes of interest), hybridization buffer, wash buffers, and sometimes amplification reagents or fluorescent readout probes. These kits may also come with positive control probes and mounting media optimized for the assay. Avantor can assist in sourcing in situ hybridization kits or custom probe libraries, connecting researchers with leading products for spatial omics assays. By using a validated hybridization kit, labs save time on probe design and can trust that the reagents will produce specific, multiplexed detection of RNA targets in the tissue.

High-quality primary antibodies against the proteins of interest are the cornerstone of spatial proteomics experiments. Depending on the study, you might label a handful of markers or deploy large panels of 10–40 antibodies for multiplex imaging. It’s important to source antibodies that are validated for IHC/IF on tissue sections (often denoted by the manufacturer). Avantor’s catalog includes a vast array of antibodies from various suppliers, so researchers can find the clones specific to their targets. For multiplex assays, consider using primary antibodies from different host species or different isotypes, which enables simultaneous detection.

Once primaries are bound, you need a way to visualize them. Secondary antibodies conjugated to fluorophores are commonly used for IF. For example, anti-mouse IgG tagged with Alexa Fluor^® dyes, or anti-rabbit IgG with FITC, etc., depending on the primary. If doing chromogenic IHC, secondary antibodies conjugated to enzymes like HRP are used along with a DAB substrate kit (diaminobenzidine chromogen) to produce a colored precipitate. In multiplex fluorescence protocols (like cyclic immunofluorescence), you might use directly labeled primary antibodies or DNA-barcoded antibodies to allow iterative or simultaneous detection. All these are consumables to plan for: fluorescent antibody kits, enzyme substrate solutions, mounting media with antifade, and even spectral calibration slides for some imaging systems. Avantor provides a broad selection of immunochemistry reagents – from single-color secondary antibodies to complete multiplex IHC kits – so labs can get all necessary detection reagents with assured compatibility.

Immunostaining workflows require several buffers (often Tris or PBS-based) for washing off unbound antibodies between steps. Additionally, blocking buffers (e.g. normal serum, BSA, or specialized protein blocking solutions) are essential consumables to prevent nonspecific binding. These reagents improve signal-to-noise by reducing background. It’s important to have buffer components that are high purity and tested for immunolabeling. Many suppliers (accessible via Avantor) offer ready-made IHC buffer packs and blocking solutions to streamline this step.

To complement molecular staining, labs often use traditional stains to provide tissue context. Hematoxylin and eosin (H&E) is commonly used either in a serial section or even on the same section (some workflows perform an H&E after transcriptomic probe extraction). A nuclear counterstain like DAPI (4’,6-diamidino-2-phenylindole) is frequently applied in fluorescent protocols to mark nuclei. These dyes are standard consumables: H&E kits, DAPI or Hoechst stain, and other specialized dyes (e.g. a collagen stain for extracellular matrix) can be included to enrich the spatial data. Avantor carries a variety of biological stains and dye reagents suitable for such purposes.