Mouse splenocytes were purchased from C\&M LABPRO. Gene Expression, TCR and BCR libraries were generated from a single channel of Chromium Connect. Libraries were prepared following the Chromium Next GEM Automated Single Cell 5' Reagent Kits v2 User Guide (CG000384).

- 10,000 cells targeted
- 10,036 cells detected
- 37,513 median reads per cell
- Sequenced on Illumina NovaSeq with 90 bp read 1, 90 bp read 2, 10 bp i5 sample barcode, and 10 bp i7 sample barcode
- Run with Cell Ranger 6.0.1


FASTQs

Multi Config CSV

Feature Reference CSV

Target Panel CSV

Loupe Browser visualization file (CLOUPE)

Gene Expression - Feature / cell matrix (raw)

Gene Expression - Feature / cell matrix HDF5 (raw)

Gene Expression - Raw per-molecule read information

Gene Expression - Genome-aligned unassigned BAM

Gene Expression - Genome-aligned unassigned BAM index

Multiplexing Analysis - Tag assignment confidence (CSV)

Multiplexing Analysis - Cells per Tag (JSON)

Multiplexing Analysis - Number of Calls per Cell (CSV)

Multiplexing Analysis - Tag Call Summary (CSV)

VDJ Ig - All contig annotations (BED)

VDJ Ig - All contig annotations (CSV)

VDJ Ig - All contig annotations (JSON)

VDJ Ig - Read-contig alignments (BAM)

VDJ Ig - Read-contig alignment index (BAI)

VDJ Ig - All-contig FASTA

VDJ Ig - All-contig FASTA index (FAI)

VDJ Ig - All-contig FASTQ

VDJ TCR - All contig annotations (BED)

VDJ TCR - All contig annotations (CSV)

VDJ TCR - All contig annotations (JSON)

VDJ TCR - Read-contig alignments (BAM)

VDJ TCR - Read-contig alignment index (BAI)

VDJ TCR - All-contig FASTA

VDJ TCR - All-contig FASTA index (FAI)

VDJ TCR - All-contig FASTQ

VDJ reference

Inputs/Library

Summary HTML

Summary CSV

Gene Expression - Loupe Browser file

Gene Expression - Genome-aligned BAM

Gene Expression - Genome-aligned BAM index

Gene Expression - Sample barcodes

Gene Expression - Feature / cell matrix HDF5 (per-sample)

Gene Expression - Feature / cell matrix (per-sample)

Gene Expression - Per-molecule read information

Gene Expression - Feature Reference

Gene Expression - Clustering analysis

Gene Expression - CRISPR analysis

Gene Expression - Target Panel

VDJ Ig - AIRR rearrangement (TSV)

VDJ Ig - Cell Barcodes (JSON)

VDJ Ig - Clonotype info (CSV)

VDJ Ig - Concatenated Segments (BAM)

VDJ Ig - Concatenated Segments index (BAI)

VDJ Ig - Concatenated Segments (FASTA)

VDJ Ig - Concatenated Segments index (FAI)

VDJ Ig - Clonotype consensus annotations (CSV)

VDJ Ig - Clonotype consensus BAM

VDJ Ig - Clonotype consensus index BAI

VDJ Ig - Clonotype consensus FASTA

VDJ Ig - Clonotype consensus index FAI

VDJ Ig - Filtered contig annotations (CSV)

VDJ Ig - Filtered contig sequences FASTA

VDJ Ig - Filtered contig sequences FASTQ

VDJ Ig - All contig info (ProtoBuf)

VDJ Ig - Loupe V(D)J Browser file

VDJ TCR - AIRR rearrangement (TSV)

VDJ TCR - Cell Barcodes (JSON)

VDJ TCR - Clonotype info (CSV)

VDJ TCR - Concatenated Segments (BAM)

VDJ TCR - Concatenated Segments index (BAI)

VDJ TCR - Concatenated Segments (FASTA)

VDJ TCR - Concatenated Segments index (FAI)

VDJ TCR - Clonotype consensus annotations (CSV)

VDJ TCR - Clonotype consensus BAM

VDJ TCR - Clonotype consensus index BAI

VDJ TCR - Clonotype consensus FASTA

VDJ TCR - Clonotype consensus index FAI

VDJ TCR - Filtered contig annotations (CSV)

VDJ TCR - Filtered contig sequences FASTA

VDJ TCR - Filtered contig sequences FASTQ

VDJ TCR - All contig info (ProtoBuf)

VDJ TCR - Loupe V(D)J Browser file

Summary

single channel

Chromium Connect

Chromium

Gene Expression

Epigenomic Profiling

Immune Profiling

Protein co-detection

Automated system for single cell partitioning, barcoding, and library preparation.

GEM-X technology-powered assays with whole transcriptome coverage to analyze immune diversity 

Universal 5'

Chromium X Series

Advanced system for multiomic analysis of hundreds to millions of cells.

5' gene expression alongside V(D)J repertoire profiling and antigen specificity of T and B cells.

Cell Ranger

Chromium Single Cell Gene Expression provides single cell transcriptome 3' gene expression and multiomic capabilities to profile tens of thousands of cells. Explore cellular heterogeneity, novel targets, and biomarkers with combined gene expression, cell surface protein expression, or CRISPR edits in each cell.

Cell Surface Protein

CRISPR Screening

Sample multiplexing

Reveal the full complexity of cellular diversity, <em>cell by cell</em>

Single Cell Gene Expression

3' gene expression profiling at scale with single cell resolution.

Chromium Single Cell Immune Profiling provides a multiomic solution to your immunology questions. Analyze full-length V(D)J sequences for paired B-cell or T-cell receptors, cell surface protein expression, antigen specificity, and/or CRISPR edits, along with gene expression, all from a single cell.

Antigen Specificity

Multiomic profiling of immune diversity, <em>cell by cell</em>

Single Cell Immune Profiling

Profile a defined set of transcripts from single cells or tissue sections with Targeted Gene Expression. Reduce costs while increasing the number of samples, or increasing sequencing depth with customizable, comprehensive gene panels.

Discontinuation of Targeted Gene Expression

Chromium Controller

Compact system for multiomic analysis of hundreds to tens of thousands of single cells.

Targeted Gene Expression

Visium

Profiling of defined transcript sets from single cells or fresh frozen tissue sections.

Analyze single cell gene expression data with a set of free, easy-to-use analysis pipelines.

Integrated GEX and VDJ analysis of Connect generated library from mouse splenocytes

FOR USE WITH

- Chromium Next GEM Automated Single Cell 5ʹ Kit v2, 24 rxns PN-1000290
- Chromium Next GEM Automated Single Cell 5ʹ Kit v2, 4 rxns PN-1000298
- Chromium Automated Single Cell Human TCR Amplification & Library Construction Kit, 24 rxns PN-1000300
- Chromium Automated Single Cell Mouse TCR Amplification & Library Construction Kit, 24 rxns PN-1000310
- Chromium Automated Single Cell Human BCR Amplification & Library Construction Kit, 24 rxns PN-1000305
- Chromium Automated Single Cell Mouse BCR Amplification & Library Construction Kit, 24 rxns PN-1000311
- Chromium Next GEM Chip K Automated Single Cell Kit, 48 rxns PN-1000289
- Chromium Next GEM Chip K Automated Single Cell Kit, 16 rxns PN-1000297
- Dual Index Kit TT Set A, 96 rxns PN-1000215


Provides instructions for constructing libraries using the Chromium Next GEM Single Cell 5' Reagent Kit (v2).

Chromium Next GEM Automated Single Cell 5ʹ Reagent Kits User Guide (v2 Chemistry)

Integrated GEX and VDJ analysis of Connect generated library from mouse splenocytes

Assess data quality

Visualize and explore data