1:1 mixture of human (GM12878, Coriell Institute) and mouse (EL4, ATCC) cells obtained by 10x Genomics were used in a classic experiment to demonstrate single cell behavior. Nuclei were isolated using the demonstrated protocol Nuclei Isolation for Single Cell ATAC Sequencing (CG000169).

ATAC libraries were generated as described in the Chromium Single Cell ATAC Reagent Kits User Guide (v1.1 chemistry) (CG000209 Rev E) using the Chromium X and sequenced on Illumina NovaSeq 6000 to approximately 90k read pairs per cell. 5,258 human nuclei and 5,889 mouse nuclei were recovered.

Paired-end, dual indexing:

- 50 cycles Read 1
- 8 cycles i7 (sample index)
- 16 cycles i5 (10x barcode)
- 49 cycles 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 X Series

Chromium

Gene Expression

Epigenomic Profiling

Immune Profiling

Protein co-detection

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

Epi ATAC

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 for identification of open chromatin regions, motif annotation, and differential accessibility analysis.

10k 1:1 Mixture of Human GM12878 and Mouse EL4 Cells, ATAC v1.1, Chromium X

FOR USE WITH:

- CG000169: Nuclei Isolation for Single Cell ATAC Sequencing
- CG000212: Nuclei Isolation from Mouse Brain Tissue for Single Cell ATAC Sequencing
- Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit, 16 rxns PN-1000175
- Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit, 4 rxns PN-1000176
- Chromium Next GEM Chip H Single Cell Kit, 48 rxns PN-1000161
- Chromium Next GEM Chip H Single Cell Kit, 16 rxns PN-1000162
- Single Index Kit N, Set A, 96 rxns PN-1000212

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Provides instructions for constructing libraries using the Chromium Single Cell ATAC Reagent Kits User Guide (v1.1 Chemistry).

Chromium Single Cell ATAC Reagent Kits User Guide (v1.1 Chemistry)

10k 1:1 Mixture of Human GM12878 and Mouse EL4 Cells, ATAC v1.1, Chromium X

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