Peripheral blood mononuclear cells (PBMCs) from a healthy donor.

Libraries were prepared following the Chromium Next GEM Single Cell ATAC Reagent Kits v1.1 (User Guide CG000209 Rev A). All PBMC libraries (v1.1 chemistry vs. v1 chemistry at all cell loads) were prepared with the same nuclei preparation.

- \~7,700 transposed nuclei were loaded. \~5,000 expected nuclei recovered. 4,585 nuclei were detected
- Sequenced on Illumina NovaSeq with approximately 41k 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 for identification of open chromatin regions, motif annotation, and differential accessibility analysis.

5k Peripheral Blood Mononuclear Cells (PBMCs) from a Healthy Donor (Next GEM v1.1)

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)

5k Peripheral Blood Mononuclear Cells (PBMCs) from a Healthy Donor (Next GEM v1.1)

Assess data quality

Visualize and explore data