Donor Information: Healthy Female.

Isolation protocol: CG000392.RevA: Isolation of Leukocytes, Bone Marrow and Peripheral Blood Mononuclear Cells for Single Cell RNA Sequencing.

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).

Sequencing data were processed using Cell Ranger, with web_summary.html and output files available in relevant tabs.

- Sequencing instrument: Illumina NovaSeq 6000
- Sequencing depth: 30,305
- 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: 4,029
- Median genes per cell: 1,644
- Median UMIs per cell: 4,739


FASTQs

Genome-aligned BAM

Genome-aligned BAM index

Per-molecule read information

Gene / cell matrix HDF5 (filtered)

Gene / cell matrix (filtered)

Gene / cell matrix HDF5 (raw)

Gene / cell matrix (raw)

Clustering analysis

Summary CSV

Summary HTML

Loupe Browser file

Web Summary

Inputs / Outputs

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

Universal 5'

Chromium X Series

Chromium

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

Gene Expression

Epigenomic Profiling

Immune Profiling

Protein co-detection

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.

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.

PBMCs from ACD-A Treated Blood Collection Tubes Isolated via SepMate-Ficoll Gradient  (5' v2 Chemistry)

_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).

PBMCs from ACD-A Treated Blood Collection Tubes Isolated via SepMate-Ficoll Gradient (5' v2 Chemistry)

Assess data quality

Visualize and explore data