Fresh cortex from adult mouse brain (P50). \~7,700 transposed nuclei were loaded and 3,880 nuclei were recovered.

Samples were sequenced on Illumina NovaSeq with approximately 44k read pairs per cell:

- 50 bp Read 1
- 8 bp i7 index (sample index)
- 16 bp i5 index (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.

Fresh Cortex from Adult Mouse Brain (P50)

Fresh Cortex from Adult Mouse Brain (P50)

Assess data quality

Visualize and explore data