Frequently Asked Questions

Our assays perform best with OCT-embedded, fresh frozen tissue sections cut at 7–10 µm and mounted on a standard 1 × 3-inch pathology slide. Well-preserved tissue morphology is critical for assay success.

The AtlasXomics team has experience with most tissue and species types, but samples that are difficult to cryosection without fixation (e.g., adipose or heavily calcified tissue), highly fibrous tissue, and very small specimens (<500 nuclei) can be challenging and may require optimization (see Q7).

Compatibility with fixed frozen and FFPE tissue types is currently in development. Please contact AtlasXomics if you are interested in learning more.

AtlasXomics offers flexible options: users can either ship samples to AtlasXomics Services for processing or receive kits to run the platform in their own lab.

Get a quote at atlasxomics.com/contact-us.

FlowGel is AtlasXomics’ next-generation spatial barcoding method, designed to simplify and enhance the original DBiT-seq workflow. While both methods are based on Deterministic Barcoding in Tissue (DBiT-seq) principles developed by the Fan Lab at Yale, FlowGel significantly streamlines the user experience.

Unlike DBiT-seq, which requires manual pipetting steps and active vacuum control, FlowGel uses pre-loaded gel-based microfluidic chips that “stamp” barcodes directly onto the tissue. This eliminates the need for pipetting, vacuum regulation, and barcode QC, reducing hands-on time and increasing throughput.

FlowGel achieves uniform barcode delivery with higher resolution (≤10 µm), supports thicker tissues (up to 15 µm), and shows matched or improved performance on key metrics such as FRiP and TSS enrichment.

1.     Project scoping call – A meeting with our sales team to define the study, establish the biological question, review tissue handling and logistics, and identify the region(s) of interest for analysis.

2.     Sample receipt and tissue qualification – Tissue-mounted slides are received on dry ice; samples are inspected and qualified for analysis.

3.     Sample or antibody optimization (optional) – Samples or antibodies are optimized using in situ bulk tests for spatial analysis.

4.     Spatial assay and sequencing – Spatial assays are performed on the tissue samples and followed by sequencing.

5.     Bioinformatics and data delivery – Data is processed, packaged, and delivered via a cloud-based platform for easy exploration. Both raw and processed data are shared with the customer for in-depth analysis.

Typical turnaround time: 6–8 weeks from slide arrival to interactive dataset. Expedited sequencing is available upon request.

AtlasXomics kits are designed to integrate seamlessly into standard molecular biology workflows. To run DBiT-seq assays, you’ll need one custom component—the AtlasXpress—which enables precise application of microfluidic chips to tissue sections. Our Spatial ATAC-seq and CUT&Tag kits include all necessary reagents and chips for in situ tagmentation and spatial barcoding.

Required lab equipment includes:

1.     Epifluorescence microscope with tiling capability (e.g., Keyence BZ-X, EVOS M7000)

2.     Access to a Next-Generation Sequencer (NGS); Spatial ATAC-seq requires 150 bp paired-end reads

3.     Incubator (37–55ºC)

4.     Standard PCR and NGS library prep tools and reagents

5.     Optional: positive pressure source to assist with slide/tissue drying

Refer to the protocol documents for full setup and workflow details.

The AtlasXomics FlowGel platform consists of three major steps: in situ chemistry to label molecules of interest, spatial barcoding using FlowGel, and library preparation for downstream sequencing. A typical user can comfortably run 2-4 samples simultaneously. Total processing time depends on the assay type, but general estimates are provided below:

Bench-side workflow timing

• In-situ chemistry
  • Hands-on time ≈ 30 min
  • Total clock time 1 – 3 days

• Spatial barcoding
  • Hands-on time ≈ 60 min
  • Total clock time ≈ ½ day

• Library preparation
  • Hands-on time ≈ 2 h
  • Total clock time ≈ 1 day

• Overall total
  • Hands-on time ≈ 4 – 5 h
  • Total clock time ≈ 3 – 5 days

Watch the 3‑min protocol video on our Resources page for a visual walk‑through.

Sequencing depth depends on tissue type, antibody target, and study goals. Use the guide below. We recommend running a shallow QC run (10–30 M reads) to check library quality before deep sequencing.

• Sample optimisation / in-situ bulk QC
  • Depth 10 M – 30 M reads
  • Purpose Confirm library quality before deep sequencing

• Spatial CUT&Tag
  • Depth 50 M – 300 M reads (≈ 15 – 90 Gb)
  • Purpose Histone PTM or transcription-factor mapping

• Spatial ATAC-seq
  • Depth 800 M – 2 B reads (≈ 240 – 600 Gb)
  • Purpose Genome-wide chromatin-accessibility profiling

Run format: 150 bp pairedend‑ on NovaSeq or NextSeq. For Ultima (single‑end, 200 bp), depth targets remain equivalent in total bases.
For large multi‑omic designs, contact us for custom depth modelling.

Yes, we do ship to countries outside of the US. Please reach out to the AtlasXomics team for more information.

We recommend that first-time kit users begin with our Sample Optimization Kit to become familiar with the platform. This step ensures:

•       Optimal permeabilization and tagmentation conditions for generating high-quality epigenome libraries

•       Verification of antibody specificity and sensitivity above IgG background in tissue (for spatial CUT&Tag)

For experienced users, our service team has extensive experience with a wide range of tissue types and antibodies. We can provide guidance on recommended conditions for specific targets and flag antibodies or tissues known to be challenging and likely to benefit from optimization.

FastQ files can be automatically processed and analyzed using our cloud-based platform. Additionally, all analysis scripts are available in our GitHub repository for convenient local use. Data processing is performed using open-source pipelines, and the resulting outputs are compatible with downstream analysis tools such as SnapATAC2, Signac, ArchR, Seurat, Scanpy, and Squidpy.

We do not recommend home‑brew reagents; AtlasXomics kits are formulated for optimal performance with AtlasXpress chips.
For bespoke applications, enquire about our Inventor Kit.

1.     Cryosection tissue at 7–10 µm and mount roughly centrally on the slide.

2.     Fix in chilled methanol and immediately store at −80 °C in a sealed slide box with desiccant.

3.     Ship on dry ice. Detailed SOP: AXO‑WI0208 Sample Prep & Mounting.

See protocol AXO-0457 FlowGel Spatial Stamping and Lysis

Precise centring maximises usable pixels; adjust positioning before lysis if needed.

Yes. DBiT‑seq is intrinsically multi‑omic. Our Inventor Kit lets advanced users print custom spatial proteomics, metabolomics, or transcriptomics barcodes. See our Cell 2023 paper on simultaneous 50‑plex protein + transcriptome mapping.

Libraries use Nextera P5/P7 indexes. Recommended run parameters:

• ATACseq: 150 PE- 800 M – 2 B reads  (≈240–600 Gb) per sample[JG1]

• CUT&Tag: see depth table above (Questions 5 & 14)
  Detailed sequences are provided in our library‑prep documentation.

See protocols 

AXO-0460 CUT-Tag Library Preparation

AXO-0459 ATAC Library Preparation