1:1 mixture of human (GM12878) and mouse (A20) cells. This is a classic human-mouse mixture experiment to demonstrate single cell behavior.

Libraries were prepared following the Chromium Single Cell ATAC Reagent Kits (User Guide CG000168 Rev B). All GM12878:A20 mixture libraries (v1.1 chemistry vs. v1 chemistry at all cell loads) were prepared with the same nuclei preparation.

- \~15,500 transposed nuclei were loaded. \~10,000 expected nuclei recovered. 4,520 human and 4,377 mouse nuclei were detected.
- Sequenced on Illumina NovaSeq with approximately 32k read pairs per cell.
  - 50 bp Read 1
  - 8 bp i7 index (sample index)
  - 16 bp i5 (10x Barcode)
  - 49 bp Read 2


FASTQs

Clustering analysis

Peak by cell matrix (filtered)

Peak by cell matrix HDF5 (filtered)

Transcription Factor by cell matrix (filtered)

Transcription Factor by cell matrix HDF5 (filtered)

Fragments (TSV)

Fragments index (TBI)

Peak annotation (CSV)

Peak-motif associations (BED)

Peaks (BED)

Position-sorted alignments (BAM)

Position-sorted alignments index (BAI)

Peak by cell matrix (raw)

Peak by cell matrix HDF5 (raw)

Per Barcode metrics (CSV)

Summary Metrics CSV

Summary Metrics JSON

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.

Epi ATAC

Chromium X Series

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

Chromatin accessibilility profiling at the single cell level.

Cell Ranger ATAC

Chromium Single Cell ATAC (Assay for Transposase Accessible Chromatin) allows you to analyze chromatin accessibility at the single cell level, providing insights into cell types and states, and deeper understanding of gene regulatory mechanisms. 

Reveal the epigenomic landscape, <em>cell by cell</em>

Single Cell ATAC

Analyze Epi ATAC data to identify open chromatin regions, motif annotation, and differential accessibility.

10k 1:1 Mixture of Fresh Frozen Human (GM12878) and Mouse (A20) Cells (v1.0)

This protocol outlines how to isolate, wash, and count nuclei suspensions for use with the Chromium Single Cell ATAC protocol. Cryopreserved primary cells (PBMCs) and cell lines (GM12878 cells; EL4 cells) were used to develop this protocol. PBMCs were cryopreserved in IMDM + 40% FBS + 15% DMSO. Cell lines were cryopreserved in RPMI + 15% FBS + 5% DMSO. Optimization of some protocol steps (e.g. lysis time, centrifugation speed/time and filtration steps) may be needed based on cell type.

<DocumentCallout>{
"This protocol is only compatible with the Chromium Single Cell ATAC reagent kits. Do not use with Multiome ATAC + Gene Expression or SC3'v3.1 assays."
}</DocumentCallout>

FOR USE WITH:

- Chromium Single Cell ATAC Reagent Kits User Guide (v1.1 Chemistry) (CG000209)
- Chromium Single Cell ATAC Reagent Kits User Guide (v1 Chemistry) (CG000168)
- Chromium Next GEM Single Cell ATAC Reagent Kits v2 User Guide (CG000496)


Outlines how to isolate, wash, and count nuclei suspensions for cell lines and PBMCs.

Nuclei Isolation for Single Cell ATAC Sequencing

10k 1:1 Mixture of Fresh Frozen Human (GM12878) and Mouse (A20) Cells (v1.0)

Assess data quality

Visualize and explore data