Summary 10X Genomics Group meeting

Meeting Overview

10x Genomics Single Cell and Spatial Biology User Group Meeting
May 2, 2024 NY

Visium HD (Spatial)
Xenium (no update here) (Spatial)
GEM-X (Transcriptome profiling)
FLEX (Probe-Based RNA Profiling)
BEAM (Barcode Enabled Antigen Mapping)
Applications in various research
proteintech

Visium HD

Visium HD is the latest spatial gene expression platform.
Official Launch: March 26, 2024 (BioSpace)

Visium HD Spatial Gene Expression: 10X Genomics

Key Features

Single-Cell Scale Spatial Resolution:
2 x 2 µm barcoded squares for whole transcriptome profiling
Chemistry : Optimized for FFPE (Formalin-Fixed, Paraffin-Embedded) and fresh frozen tissues
Integration with Histological Data:
Combine H&E or IF images with high-resolution transcriptomic data from the same tissue section.
Software : Space Ranger(processing) and Loupe Browser(visualize)

Comparison between Visum and Visium HD

GEM-X

GEM-X is the next-generation technology architecture from 10x Genomics, improving upon the earlier Next GEM architecture used in previous Chromium assays.

Assays by GEM-X:

Chromium GEM-X Single Cell Gene Expression v4:

3’ whole-transcriptome profiling
Combines gene expression profiling with cell surface protein detection using feature barcode technology
GEM-X technology

Feature Barcode Technology uses oligo-tagged antibodies to measure protein expression on the cell surface alongside transcriptomics data
Combination with Cell surface proteins tagging using tens to hundreds of antibodies.
Applications classify immune cell subtypes and states.

GEM-X Single Cell Immune Profiling v3:

Multiomic profiling to map adaptive immune responses. Delivers up to 80% cell capture efficiency and improved pairing of full-length T- and B-cell receptor sequences.

Enhanced Sensitivity and Capture Efficiency:
Rare cell types and low-RNA content cells like neutrophils
Mapping T-cell and B-cell receptor sequences.
Lower Multiplet Rate: Reduces multiplet rates with improved GEM-X microfluidic chips.

GEM-X SC3’v3 vs v4

FLEX

A cutting-edge platform designed to enable single-cell RNA sequencing on previously inaccessible samples. By leveraging fixation technology and a comprehensive probe-based approach, FLEX makes it possible to profile gene expression in formaldehyde-fixed, FFPE, and frozen samples.

For challenging sample types
Fixed sample or fixation-based

Key Features

Works with fresh, frozen, and formalin-fixed, paraffin-embedded (FFPE) samples. Suitable for whole tissues, cell suspensions, and nuclei.
Probe-Based RNA Profiling:

Probe sets targeting predetermined transcript regions.
Currently available for human (18,082 genes) and mouse (19,059 genes) transcriptomes.
- Human probe set
- Mouse probe set
Simultaneous Surface Protein Detection: Integrates feature barcode technology for surface protein profiling.
Sample Fixation and Storage: Samples can be safely stored or transported without compromising data quality. Fixation at the point of collection preserves the biological state.

Compatible with Illumina NextSeq and NovaSeq platforms

More info at FLEX 10X Genomics

BEAM (Barcode Enabled Antigen Mapping)

antigen-specific B- and T-cell clonotypes. Built on the Chromium Single Cell Immune Profiling platform
Antigen-Specific Discovery:
- BEAM-Ab: Identifies antigen-specific B-cell clonotypes.
  (BEAM-Ab provides full-length paired B-cell receptor sequences)
- BEAM-T: Identifies antigen-specific T-cell clonotypes.
- Comprehensive profiles including full-length paired V(D)J sequences, gene expression, and cell surface proteins.

BEAM at 10X Genomics

Summary Table

Platform	Purpose	Primary Application	Sample Compatibility	Key Data Output
FLEX	scRNA-seq from fixed tissues	Gene expression and protein detection	Fresh, frozen, fixed	Gene expression and surface protein data
Visium HD	Spatial transcriptomics	Spatial mapping of gene expression	Fresh frozen, FFPE	Spatial maps of gene expression
GEM-X	High-throughput scRNA-seq	Single-cell profiling, immune profiling	Fresh tissues	Gene expression, immune receptor sequencing
BEAM	Antigen-specific B- and T-cell discovery	Antigen screening of immune repertoires	PBMCs, splenocytes, lymph node aspirates	Full-length paired V(D)J sequences, gene expression

Single-cell immune profiling technologies

BEAM vs Evercode (Parse Bioscience)

Evercode release event (Boston, May 2024)

Evercode link

Single-cell immune profiling technologies by Parse Biosciences and the BEAM technology by 10x Genomics:

Feature	Parse Biosciences Single-Cell Immune Profiling	10x Genomics BEAM
Technology	Uses split-pool combinatorial barcoding system	Barcode-enabled antibody mapping
Points	- No specialized equipment needed - Capable of profiling up to one million cells - Simultaneous BCR and TCR sequencing with gene expression profiling	- Focus on cell surface protein profiling - Precise analysis of protein expression changes among different immune cells
Applications	- Simultaneous profiling of TCR and BCR - Detailed analysis of adaptive immune responses	- Immune cell phenotyping - Analyzing protein expression variations among immune cells
Advantages	- Scalable to large numbers of samples and cells - Can be used with fixed cells and nuclei	- High specificity for cell surface antigens - Allows simultaneous analysis of multiple cell markers

proteintech

MultiPro Fixed Cell Immune Profiling Antibody Cocktail

product link
PROT/RNA comparison

Product Overview: The MultiPro™ cocktail contains 53 antibodies that target a mix of intracellular and surface proteins, plus 5 isotype controls.
Cellular Analysis Tool: Analyzing cellular components in single-cell RNAseq experiments.
Compatibility: Compatible with the 10x Genomics® Chromium® Single Cell Gene Expression Flex product.
Dual Detection: Simultaneous capture of protein and gene expression profiles from the same cell, enhancing the depth of cell state analysis.
Intracellular Protein Research: Marks significant progress in the field by overcoming previous challenges in accessing intracellular proteins in single-cell studies.