The BioMicro Center supports two complementary approaches to spatial transcriptomics: 10x Visium HD from 10x Genomics for slide-based spatial gene expression, and AVITI24 in situ sequencing from Element Biosciences. The choice of method depends on your tissue type, resolution requirements, and experimental goals. We strongly encourage consultation with BMC staff prior to beginning a spatial experiment.
10x Visium HD is a spatial transcriptomics platform that profiles whole-transcriptome gene expression across intact tissue sections at single-cell-scale resolution. Tissue sections are processed through the CytAssist instrument, which transfers RNA complexes onto a capture slide containing a continuous array of 3,000,000 spatially barcoded 2 µm squares covering a 6.5 × 6.5 mm capture area (~0.65 cm²). Two chemistries are available: a probe-based assay for human and mouse (FF, FxF, and FFPE), and a polyA-based assay (Visium HD 3') for fresh frozen tissue from any species. H&E or immunofluorescence (IF) staining can be performed prior to processing for protein co-detection.
ARRAY SPECIFICATIONS
Capture area
6.5 × 6.5 mm (~0.65 cm²) per tissue
Spots
3,000,000 barcoded squares
Spot size
2 µm continuous (no gaps)
Default analysis bins
8 µm and 16 µm (SpaceRanger); custom bins supported
Tissues per slide
2
Multiomics
H&E or IF staining prior to processing; antibody panels (FFPE, human only)
CHEMISTRY OPTIONS
Visium HD (probe-based)
Visium HD 3' (polyA-based)
Species
Human, Mouse only
Any species
Tissue formats
Fresh Frozen (FF), Fixed Frozen (FxF), FFPE
Fresh Frozen (FF) only
Notes
~3 probes per gene; exogenous sequences (GFP, reporters) require custom probes. A small fraction of genes are excluded by default due to predicted off-target activity: human excluded gene list (~2.1%), mouse excluded gene list (~1.8%).
Sectioning & H&E performed by the Tang Histology Facility (KI). Coordinate with BMC staff to arrange.
For current pricing, see BioMicroCenter:Pricing → Single Cell & Spatial Services → Visium. Sequencing is charged separately; 400–800M reads per tile recommended for Visium HD.
FAQs for Users 1) What tissues are compatible?
Visium HD (probe-based) supports human and mouse tissues in FF, FxF, and FFPE formats. Visium HD 3' (polyA) supports fresh frozen tissue from any species. 10x Genomics maintains a list of tested tissues. Additional optimization may be required for tissues with high fat content. Consult BMC staff before starting.
2) How do I prepare and submit tissue?
Tissue sectioning and H&E staining are performed by the Hope Babette Tang (1983) Histology Facility at the Koch Institute. Coordinate with both the Histology Facility and BMC staff before your first submission. FF tissue should be embedded in OCT and stored at −80°C; FFPE blocks at room temperature.
3) What is the resolution?
Visium HD captures data at 2 µm bin resolution (single-cell scale). SpaceRanger aggregates into 8 µm and 16 µm bins for higher sensitivity by default; custom bin sizes are also supported. Cell segmentation based on H&E imaging is available in the Loupe Browser pipeline.
4) How much sequencing is needed?
400–800M reads per tile is recommended for Visium HD. Sequencing is submitted separately via iLabs. Compatible platforms include NovaSeq SP, NovaSeqX, and Element AVITI. Discuss read depth with BMC staff based on your tissue type and goals.
5) Does Visium HD require permeabilization optimization?
No. Visium HD does not require permeabilization time optimization. For fresh frozen tissues new to the platform, a test array is available to verify tissue quality and placement before committing a full experiment.
6) Can I detect proteins alongside gene expression?
Yes. H&E or IF staining can be performed prior to CytAssist processing. Antibody panels for protein co-detection (human tissues, FFPE only) are available from 10x Genomics. Discuss your experimental design with BMC staff in advance.
7) What analysis outputs are provided?
The BMC delivers FASTQ files, aligned BAM files, the spatial feature-barcode matrix (raw and filtered at 2, 8, and 16 µm bins), and a Loupe Browser file. Downstream informatics support is available through BMC staff.
8) Can I combine Visium HD with single-cell data?
Yes. Visium HD data integrates with single-cell or single-nucleus RNA-seq (e.g., 10x Chromium Flex) for cell-type deconvolution. Starting from the same tissue block, nuclei can be isolated for Flex single-cell gene expression. Coordinate with BMC staff if planning a multi-modal experiment.
9) My gene of interest is exogenous (GFP, reporter, viral) or missing from the probe set. What are my options?
The probe-based Visium HD assay does not capture exogenous sequences by default. Custom probes can be designed for detection — see 10x Genomics technical note CG000621. Additionally, a small fraction of endogenous genes are excluded from the standard probe sets due to predicted off-target activity: see the human excluded gene list (~2.1% of genes) and mouse excluded gene list (~1.8% of genes). Alternatively, the polyA-based Visium HD 3' assay captures all polyadenylated transcripts and does not require custom probes.
AVITI24 CYTOPROFILING & IN SITU SEQUENCING
Beta Service — Early Access: The AVITI24 Teton CytoProfiling and DISS services at the BioMicro Center are operational but not yet routine. Parameters, pricing, and workflows are still being established. Consultation with BMC staff is required before submitting samples.
The BioMicro Center provides access to the Element Biosciences AVITI24 platform for in situ single-cell multiomics. Using Teton™ CytoProfiling, the instrument co-detects RNA transcripts, proteins (including phospho-proteins), and cell morphology at subcellular resolution — directly in intact cells, without library preparation. Targeted in situ sequencing via Direct In Sample Sequencing (DISS) can be run simultaneously in the same experiment. Because this is an early-access service, results and run parameters are less well-established than our established offerings. Consultation with BMC staff is strongly encouraged before designing experiments.
MAPK Cell Cycle · MAPK Apoptosis · Immuno-Oncology · Neuroscience mix up to 3 panels per run; consult staff for latest
User-designed probes
User-designed or polyT probe
Teton CytoProfiling and DISS (low output) can be run simultaneously in the same experiment. Custom antibody add-ons require unconjugated rabbit monoclonal primaries. Consult BMC staff for current options.
SAMPLE REQUIREMENTS
Supported
Monolayer cell culture (adherent); pelleted cell suspension (spun down and resuspended)
Not yet supported
Complex 3D culture, organoids, tissue sections — contact BMC to discuss future availability
Cell density
Consult BMC staff; optimized per cell type
Species
Human (all current fixed panels); other species — consult staff regarding panel compatibility
SUBMISSION
Submission via iLabs is not yet available. Contact BMC staff directly to discuss your experiment before scheduling. Consultation is required for all AVITI24 Teton and DISS submissions.
About the Service
The AVITI24 at BMC supports Teton™ CytoProfiling — an in situ multiomics approach that co-detects RNA transcripts, proteins (including phospho-proteins), and cell morphology directly inside intact cells on the flow cell. Each run cycles through Cell Painting (morphology imaging), antibody scoring, and in situ sequencing rounds without any library preparation. A full run takes 24–48 hours end-to-end with approximately 45 minutes of hands-on time, capturing ~100–200 transcripts per 100 µm² at subcellular resolution.
The platform is designed for cells in monolayer culture or spun-down suspension. It profiles up to 350 RNA targets, ~18 protein targets, and 6 morphology channels simultaneously in a single experiment — giving a co-registered multiomic readout per cell that would otherwise require separate assays on separate instruments.
Targeted in situ sequencing (DISS, low output) can be layered onto any Teton run. This uses a user-designed probe (~50 nt, 1 priming event) to detect specific sequences in situ — useful for CRISPR guide detection, barcode readout, or expressed mutation calling. Note that reads are too short for TCR/BCR sequencing; consult BMC staff if your application involves immune repertoire.
Available Assays
BMC supports all four currently available fixed Teton panels (MAPK Cell Cycle, MAPK Apoptosis, Immuno-Oncology, Neuroscience). Up to three panels can be combined per run, giving up to 350 RNA targets and ~18 usable protein targets in a single experiment. Custom antibody add-ons are possible using unconjugated rabbit monoclonal primary antibodies — no conjugation or barcoding required. Discuss panel selection with BMC staff; reagent availability and lead time vary.
Data Outputs
The BMC provides core analysis outputs including:
Cell-by-gene expression matrix (350 transcript targets per panel)
Cell-by-protein parameter data (~18 antibody targets)
Morphology feature data per cell (nucleus, actin, membrane; ER, Golgi, mitochondria for human)
Additional informatics support is available through BMC staff.
Pricing
Pricing for AVITI24 Teton CytoProfiling and DISS is not yet finalized. See BioMicroCenter:Pricing for updates as pricing is established. Sequencing-only runs on the AVITI24 are charged at standard AVITI24 sequencing rates.
Service Status
This service is in beta. The instrument is operational and BMC has completed initial runs, but experimental parameters are still being validated. We welcome early users willing to work collaboratively with BMC staff to establish protocols.
