10x Genomics
Chromium Single Cell Gene Expression

Cell Ranger3.0, printed on 12/22/2024

Glossary of Terms

Entries are ordered alphabetically. These definitions may be specific to the usage of these terms in the context of Feature Barcoding.

Single Cell RNA-seq

GEM well (or GEM group): A set of partitioned cells (Gelbeads-in-Emulsion) from a single 10x Chromium™ Chip channel. One or more sequencing libraries can be derived from a GEM well.

Library (or Sequencing Library): A 10x-barcoded sequencing library prepared from a single GEM well. With Feature Barcoding or V(D)J assays, it is possible to create multiple libraries from the same GEM well. The library types may inclue Gene Expression, Antibody Capture, CRISPR guide capture, TCR-enrichment, etc.

Sample: A cell suspension extracted from a single biological source (blood, tissue, etc).

Sequencing Run (or Flowcell): A flowcell containing data from one sequencing instrument run. The sequencing data can be further demultiplexed by lane or by sample indices.

Feature Barcoding Technology

Feature Barcoding Antibody (or Antibody): Refers to a Feature Barcoding reagent consisting of an antibody with high affinity to a known Cell Surface Protein coupled to a Feature Barcode oligo that identifies the antibody. These reagents are used to quantify the expression of cell surface proteins. For example, the TotalSeq™-B product line is a family of Feature Barcoding antibodies that are compatible with the Single Cell 3' v3 solution.

Cell Surface Protein: a protein that is localized to the cell membrane, typically containing extracellular domains. These proteins can be quantified with Barcoded Antibodies.

CRISPRa (or CRISPR activation): Similar to CRISPRi, but uses a Cas9 fused to an activating domain to promote expression of target gene instead of repressing it.

CRISPR Guide RNA: See sgRNA

CRISPRi (or CRISPR Interference): A method for measuring the impact of perturbations to gene expression levels. sgRNAs with protospacers targeting a gene of interest are used with a non-cutting Cas9 that is fused to a repressive domain. This represses the expression of the selected gene.

Count Matrix (or Feature-Barcode Matrix): Formerly known as the Gene-Barcode Matrix. A matrix of counts representing the number of unique observations of each feature within each cell barcode. Genes defined by the transcriptome reference and Feature Barcodes defined in the Feature Reference appear as rows in the matrix. Each barcode is a column of the matrix.

CROP-Seq: An assay scheme for pooled CRISPRi and CRISPRa experiments with single-cell Gene Expression readout. See Datlinger et al., Nature Methods 2017

Dextramer: Refers to a Feature Barcoding reagent consisting of multiple copies of a peptide-MHC (p-MHC) complex conjugated to a Dextran backbone, coupled to a DNA oligo carrying a Feature Barcode that identifies the peptide-MHC complex. The p-MHC complex is the antigen of a T-Cell Receptor. Dextramers compatible with 10x Genomics Feature Barcoding are supplied by Immudex.

Feature: A unique type of countable molecule. Can refer to a gene, an barcoded antibody, a CRISPR Guide RNA or another barcoded reagent. Each feature is either a gene declared in the transcriptome reference or a feature barcode declared in the feature reference file. Corresponds to a row in the Count Matrix.

Feature Barcode: The subsequence of a Feature Barcoding read that uniquely identifies the identity of the Feature Barcoding reagent.

Feature Reference: A CSV file declaring the name, read layout, and barcode sequence of the all the Feature Barcoding reagents in use in an experiment. A Feature Reference CSV must be provided to cellranger count when using Feature Barcoding. See the Feature Reference Documentation for details.

Guide RNA (or sgRNA, or Single Guide RNA): The Guide RNA, along with a Cas9 enzyme form the CRISPR system. The protospacer region of the Guide RNA recognizes a particular sequence in the genome.

p-MHC (or Peptide-MHC): An antigen-presenting MHC gene, bound to a displayed peptide. These complexes are recognized by T-Cell receptors in the adaptive immune system. Dextramers are Feature Barcoding capable p-MHC reagent technology.

Perturb-Seq: The original demonstration of a pooled CRISPRi assay with a single-cell Gene Expression readout, using barcodes to identify which CRISPRi perturbations were present in each cell. See Dixit et al., Cell 2016.

Protospacer: The portion of CRISPR Guide RNA (sgRNA) that is complementary to the genome and determines the specificity of the sgRNA. The protospacer sequence itself is read as the Feature Barcode in CRISPR applications.