Cells from a combined cortex, hippocampus and sub ventricular zone of an E18 mouse (the same cells were used to generate [5k_neuron_v3](/datasets/5-k-cells-from-a-combined-cortex-hippocampus-and-subventricular-zone-of-an-e-18-mouse-v-3-chemistry-3-1-standard-3-0-2)).

Libraries were prepared following the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 User Guide (CG000204 RevA).

- 6,566 cells detected
- Sequenced on Illumina NovaSeq with approximately 78,597 reads per cell
- 28bp read1 (16bp Chromium barcode and 12bp UMI), 91bp read2 (transcript), and 8bp I7 sample barcode
- run with --expect-cells=5000


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

Files

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 gather broad information from diverse species

Universal 3'

Chromium X Series

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

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

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

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

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

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.

5k Cells from a combined cortex, hippocampus and subventricular zone of an E18 mouse (Next GEM)

FOR USE WITH:

- Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1, 16 rxns PN-1000121
- Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1, 4 rxns PN-1000128
- Chromium Next GEM Chip G Single Cell Kit, 48 rxns PN-1000120
- Chromium Next GEM Chip G Single Cell Kit, 16 rxns PN-1000127
- Single Index Kit T Set A, 96 rxns PN-1000213

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5k Cells from a combined cortex, hippocampus and subventricular zone of an E18 mouse (Next GEM)

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