-
What is Xenium?
What is Xenium?
The 10X Genomics Xenium Analyzer will support true single cell spatial transcriptomics on fresh frozen or fixed tissue samples. You can characterize 100s to 1000s of RNAs in cells and tissues using customizable pre-designed or fully custom gene panels. The Xenium uses a high sensitivity, padlock probe rolling circle amplification (RCA) technology to quantify mRNAs in single cells within tissues. This technology supports high sensitivity detection of transcripts across a range of expression levels, including rare transcripts. The methodology can be used to detect short/highly degraded transcripts (as commonly seen after tissue fixation) and can distinguish between closely related transcripts (e.g. isoforms of genes). Tissue samples are arrayed on Xenium slides (2 slides/run with 12 x 24 mm imageable area/slide). Validated gene probes are selected (custom and off the shelf containing gene specific barcodes, can use 50-5000 probe sets/run); hybridized to the slide, ligated and amplified using RCA. The slide is loaded into the Xenium analyzer where the amplified products are detected through successive rounds of fluorescent probe hybridization that take 2 days to complete. An optical signature specific for each gene is generated and then spatially mapped to the transcripts across the tissue section. The Xenium data can be visualized using freely available “explorer” tools that allow for run QC as well as simple exploration of the datasets.
For more information concerning the Xenium’s abilities and innovations please click here.
-
Sample Prep
Sample Prep
10x Genomics Technical Documentation is available here.
Xenium slides include an imageable area outlined by a white line measuring 12 mm x 24 mm, with an available sample positioning area measuring 235 mm2 (10.45 mm x 22.45 mm).
The Sample Area is surrounded by fiducials. Tissue sections are placed within the Sample Area without obstructing the fiducials. The imageable area includes the area within the fiducial frame + Sample Area.
The Sample Area can accommodate as many tissue sections as can fit within the space. Ensure tissue sections (including wax) DO NOT overlap with fiducials or other tissue sections.
For multiple samples, embedding tissues into the same block would be helpful. The co-embedded block must be exclusive to the panel, not the tissue. Also, two different panels can be selected for the same Xenium Analyzer run (one panel per slide).
There are protocols available for cultured cells and PBMCs.
-
Custom Probe Design
Custom Probe Design
10x Genomics Technical Documentation is available here.
Human and Mouse custom probes can be designed online with the Xenium Panel Designer.
Advanced Custom options are available for species other than mouse and human for designs against isoforms, SNVs or exogenous genes.
Typically need a minimum of 80 nucleotides to consider for custom probe design so things like miRNAs are likely not possible.
Public single cell data sets or user provided single cell data sets should be used to guide in the custom probe design. Differences in expression levels of genes within any given panel may influence how many probes will be designed against each gene target.
-
Xenium Pricing
Xenium Pricing
Choose from the following three options:
- 10X Xenium genes using off-the-shelf predesigned gene panel +/- 1-100 add-on genes (page 1 below) OR
- 10X Xenium 1-480 genes using custom stand-alone gene panel (page 2) OR
- 10X Genomics Xenium Prime (5K gene panel +/- add-on genes) (page 3)
I. 10X Genomics Xenium (off-the-shelf panel; 1-100 add-on genes)
BASIC SERVICE Fees with an off-the-shelf panel
Off-the-shelf currently includes choice of 9 predesigned panels of 247-380 genes in human immuno-oncology, multi-tissue cancer, breast, brain, lung, skin, colon and mouse tissue atlassing and brain.
Xenium Kit, 2 reactions
Cell segmentation staining kit, 2 reactions
Shipping
Machine run
Labor and Service Fee
Experimental consultation and set up
Pre-designed gene panel ($345-$700), 2 reactions
5,842
1,472
300
803
1,577
332
700
1 xenium run (2 slides) cost with a 10X pre-designed off-the-shelf panel
$11,026
Add-on panels
(To be used with off-the -shelf panel)
1-50 add-on genes (4 reactions; ½ will be left over)
3,550
1 xenium run (2 slides) cost with 50 add-on panel [Basic Fee + 50 add-on genes]
$14,576
51 - 100 add-on genes (4 reactions; ½ will be left over)
5,650
1 xenium run (2 slides) cost with 100 add-on genes panel [Basic Fee + 100 add-on genes]
$16,676
II. 10X Genomics Xenium (1 – 480 gene panel using custom stand-alone panel)
BASIC SERVICE Fees for stand-alone panel
Xenium Kit, 2 reactions
cell segmentation staining kit, 2 reactions
shipping
Machine run
Labor and Service Fee
Experimental consultation and set up
5,842
1,472
300
803
1,577
332
1 xenium run (2 slides) cost
$10,326
Stand-alone panel custom genes (To be used without off-the -shelf panel)
1-50 add-on genes (4 reactions; ½ will be left over)
3,550
1 xenium run (2 slides) cost with 50 add-on panel [Basic Service Fee + 50 add-on genes]
$13,876
51 - 100 add-on genes (4 reactions; ½ will be left over)
5,650
1 xenium run (2 slides) cost with 100 add-on genes panel [Basic Service Fee + 100 add-on genes]
$15,976
101-300 custom genes (4 reactions; ½ will be left over)
11,600
1 xenium run (2 slides) cost with 300 custom genes panel [Basic Service Fee + 300 add-on genes]
$21,926
301 – 480 add-on genes (4 reactions, ½ will be left over)
17,850
1 xenium run (2 slides) cost with 480 custom genes panel [Basic Service Fee + 480 add-on genes]
$28,176
III. 10X Genomics Xenium Prime (5K gene panel)
Xenium Prime Kit, 2 reactions (includes Xenium Kit, 2 rxns; cell segmentation staining kit, 2 rxns; and 5K gene panel)
Shipping
Machine run
Labor and Service Fee
Experimental consultation and set up
13,800
300
803
1,577
332
1 xenium prime run (2 slides) cost with the 5K gene panel [Basic Service Fee + 5K panel]
$16,812
Add-on genes for Prime
(To be used with the 5K panel)
1-50 add-on custom genes (12 reactions; 83% will be leftover)
4,000
1 xenium prime run (2 slides) cost with 5K + 50 add-on gene panel
$20,812
51 - 100 add-on custom genes (12 reactions; 83% will be leftover)
7,000
1 xenium prime run (2 slides) cost with 5K + 100 add-on gene panel
$23,812
-
U-BDS Consultation, Data Analytics and Visualization Pricing for Xenium
U-BDS Consultation, Data Analytics and Visualization Pricing for Xenium
Task and sub tasks
Rate
Total Cost
REQUIRED for ALL U-BDS services: Initial Consultation – 2 hours
This session includes a review of experimental design, probe list (including the 10X Genomics report), and scope assessment. Additional consultations, if necessary, can be scheduled at the PI’s expense
$100/hr
$200
TIER I SERVICE
This foundational service includes:
- Raw data quality and control (QC) and removal of low-quality cells
- Data normalization (including area normalization)
- Data integration across samples
- Preliminary tissue domain segmentation through repeated runs across multiple parameter configurations
- Preliminary cell clustering and cell marker expression through repeated runs across multiple parameter configurations
Deliverables:
- Seurat object, accompanying metadata, and figures for the analysis described above
$5,000 all inclusive of services listed for Tier I
$5,000
Initial Consultation of $200 is a prerequisite for Tier I Services
TIER II SERVICE
This advanced service requires completion of Initial Consultation and Tier I Service. Tier II Service covers 60 hours of hands-on analyst time for tertiary analysis going beyond analysis and deliverables from Tier I Service.
U-BDS encourages the PI and labs to carefully review outputs from the Tier I Service endpoints for selection of tissue segmentation and cell typing. Advanced review will make the best use of these hours by focusing on the next analytical steps rather than re-iterations of cell typing/segmentation. (Of note: Tier I service can be performed with later initiation of Tier II with appropriate review and consideration).
Hourly block may be used for:
- Anatomical annotation superimposition to transfer anatomical regions (based on manual annotations / pathologist annotation) into tertiary analysis
- Cell label transfer
- Parameter choice (based off results and review from Tier I service) for tissue segmentation and cell cluster calls
- Identification of cell proportions by variable(s) of interest (e.g.: tissue segmentation, experimental variable etc.)
- Differentially Expressed Genes (DEG) identification across condition(s) of interest
- Pseudobulk approaches will be implemented as the primary test for DEG analysis. Experimental replicates are required.
- Generation of figures related to standard analysis processing (e.g.: UMAPs, volcano plots etc.).
- GO and pathway analysis results from DEG analysis of interest.
- Report generation summarizing analytical findings
$9,000 for 60 hr of hands-on analyst time
$9,000
Initial Consultation of $200 and Tier I Service of $5,000 are prerequisites for Tier II Services
Constraints:
- Time block limit: The 60-hour block may not be sufficient for all analysis types and experimental designs outlined above, as the required hands-on time depends on analytical decisions informed by the outputs from the Tier I service (e.g.: U-BDS involvement in refinement of cell typing, markers or reference refinement incur hours). If additional time is needed beyond the initial 60 hours, PIs may purchase additional hourly blocks at their expense.
- Note: U-BDS will cap fee-for-service hourly blocks at 200 hours. Any work exceeding this limit must transition to U-BDS’s collaborative model (% effort). Of note, a collaborative model can be initiated at any stage - reaching 200 hours is not a prerequisite.
- Turn-around times are contingent on the following:
- High-Performance Computing downtime (whether planned or unplanned).
- Employee-related limitations (e.g.: vacation time, sick days, holidays etc.)
- Core staff and director availability as employees work with other core projects and tasks.
- Other analyses and independent U-BDS activities in which the core staff/directors aid or participate (e.g.: workshops, new consultations, weekly office hours, etc.)
- Data quality issues.
Assumptions of dataset:
- Panel design meets assumptions required for study.
- Panel design should not be heavily skewed towards a subset of cell types (representative panel design is critical).
- Panel design meets requirements for a successful Xenium run with no or minimum impact on QC.
- 10X Xenium multimodal sample preparation is required for higher fidelity in cell segmentation
- Data is of sufficient quality.
- Study design meets assumptions for analytical steps and tools.
- RNA and cell quality are sufficient for analysis.
- All data passes QC:
- Assignments to known features (probe list) should be sufficient for tertiary analysis.
- Number of cells per sample should be sufficient for tertiary analysis.
- Number of genes/features detected per cell should be sufficient for tertiary analysis.
- Number of biological samples retained after quality and control should be sufficient for tertiary analysis (e.g.: no samples, or minimal samples removed due to quality of sectioning or other factors affecting quality of data).
- Batch effects, if any, were minimized during sample preparation among all samples (e.g.: sample distribution across slides were balanced among group to avoid confounding).
- Altered timelines related to the impact of failed QC or other failures, or the need for additional data processing not described here will both incur additional costs and extend the timelines.
Deliverables not included in Scope:
- Visualizations beyond what is stated under “Tasks” will need to be discussed, amended, and approved as part of the SOW process (which can incur additional costs).
- Assistance with creation of panel design is not included.
- Assistance with data uploads to public databases is not included.
- Assistance with grant writing.
- Outputs from additional tertiary analysis from spatial transcriptomics (including Xenium) beyond what is stated are not included (e.g.: ligand-target prediction etc.)
- Personalized training to the laboratories involved in this project is not included.
- Items related to refinement of panel design are not included.