C57Bl/6 mouse splenocytes were obtained by 10x Genomics from C\&M Lab Pro. Whole transcriptome/Gene Expression libraries were generated as described in the Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index) User Guide (CG000331 Rev A). This whole transcriptome library was used as the parent library for downstream target enrichment. Data were analyzed with Cell Ranger 6.0.1.

- Sequencing instrument: Illumina NovaSeq 6000
- Sequencing depth: 46,637 mean reads per cell
- Sequencing configuration: Paired-end (28 X 90), single-indexed. Read 1: 28 cycles (16 bp barcode, 10 bp UMI); i7 index: 10 cycles; i5 index: 10 cycles; Read 2: 90 cycles (transcript).
- Cells detected: 1,358
- Median genes per cell: 1,844
- Median UMIs per cell: 4,372


FASTQs

Feature Reference CSV

Library CSV

Target Panel

Genome-aligned BAM

Genome-aligned BAM index

Per-molecule read information

Feature / cell matrix HDF5 (filtered)

Feature / cell matrix (filtered)

Feature / cell matrix HDF5 (raw)

Feature / cell matrix (raw)

Clustering analysis

CRISPR analysis

Summary CSV

Summary HTML

Loupe Browser file

Summary

Mouse Splenocytes: 5’v2 Whole Transcriptome Analysis

Mouse Splenocytes: 5’v2 Targeted, Custom Immunology Panel

Chromium Controller

Chromium

Gene Expression

Epigenomic Profiling

Immune Profiling

Protein co-detection

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

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 Connect

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

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.

_Depending on your experimental goals, additional Library Construction Kits (PN-1000190) may be required. Please click [here](https://kb.10xgenomics.com/hc/en-us/articles/360048287712-When-do-I-need-an-additional-Library-Construction-Kit-PN-1000190-to-run-my-experiment-with-Next-GEM-5-v2-reagent-kits) for further guidance._

FOR USE WITH:

- Chromium Next GEM Single Cell 5' Kit v2, 16 rxns PN-1000263
- Chromium Next GEM Single Cell 5' Kit v2, 4 rxns PN-1000265
- Library Construction Kit, 16 rxns PN-1000190
- Chromium Single Cell Human TCR Amplification Kit, 16 rxns PN-1000252
- Chromium Single Cell Human BCR Amplification Kit, 16 rxns PN-1000253
- Chromium Single Cell Mouse TCR Amplification Kit, 16 rxns PN-1000254
- Chromium Single Cell Mouse BCR Amplification Kit, 16 rxns PN-1000255
- Chromium Next GEM Chip K Single Cell Kit, 48 rxns PN-1000286
- Chromium Next GEM Chip K Single Cell Kit, 16 rxns PN-1000287
- Dual Index Kit TT Set A, 96 rxns PN-1000215


Provides instructions for constructing libraries using the Chromium V(D)J Single Cell 5' Reagent Kit (v2).

Mouse Splenocytes: 5’v2 Whole Transcriptome Analysis

Assess data quality

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