
**Biomaterials**

Peripheral blood mononuclear cells (PBMCs) from a healthy donor were obtained by 10x Genomics from AllCells.

**Sample preparation**

Cryovials were thawed following the Direct Media Thawing protocol within the Cell Thawing Protocols for Single Cell Assays Handbook ([CG000447](/support/universal-three-prime-gene-expression/documentation/steps/sample-prep/cell-thawing-protocols-for-single-cell-assays)).

**Assay workflow**

Gene Expression libraries were generated as described in the Chromium GEM-X Single Cell 5' Reagent Kits v3 User Guide ([CG000733](/support/universal-five-prime-gene-expression/documentation/steps/library-prep/chromium-gem-x-single-cell-5-v3-gene-expression-user-guide)).

**Sequencing**

Libraries were sequenced on an Ultima UG 100™ sequencer following the UG 100 Solaris™ Flex workflow to 42,079 reads per cell (downsampled).

**Analysis**

Cell Ranger v9.0.1 was used to map reads to the probe set and output feature-barcode matrices for further analysis.

**How to view data**

To get started, download [Loupe Browser](/support/software/loupe-browser/downloads) to explore the Loupe file, or read more about the other [Cell Ranger outputs](/support/software/cell-ranger/latest/analysis/outputs/cr-5p-outputs-overview-multi).


FASTQs

Multi Config CSV

Feature Reference CSV

Target Panel CSV

Sample Images

Loupe Browser visualization file (CLOUPE, raw)

Gene Expression - Feature / cell matrix (raw)

Gene Expression - Feature / cell matrix HDF5 (raw)

Gene Expression - Raw per-molecule read information

Gene Expression - Genome-aligned unassigned BAM

Gene Expression - Genome-aligned unassigned BAM index

Multiplexing Analysis - Tag assignment confidence (CSV)

Multiplexing Analysis - Cells per Tag (JSON)

Multiplexing Analysis - Number of Calls per Cell (CSV)

Multiplexing Analysis - Tag Call Summary (CSV)

VDJ Ig - All contig annotations (BED)

VDJ Ig - All contig annotations (CSV)

VDJ Ig - All contig annotations (JSON)

VDJ Ig - Read-contig alignments (BAM)

VDJ Ig - Read-contig alignment index (BAI)

VDJ Ig - All-contig FASTA

VDJ Ig - All-contig FASTA index (FAI)

VDJ Ig - All-contig FASTQ

VDJ TCR - All contig annotations (BED)

VDJ TCR - All contig annotations (CSV)

VDJ TCR - All contig annotations (JSON)

VDJ TCR - Read-contig alignments (BAM)

VDJ TCR - Read-contig alignment index (BAI)

VDJ TCR - All-contig FASTA

VDJ TCR - All-contig FASTA index (FAI)

VDJ TCR - All-contig FASTQ

VDJ reference

Multiplexing Analysis - FRP GEM Barcode Overlap (CSV)

Gene Expression - Probe barcode matrix HDF5 (raw)

Library Inputs/Outputs

Summary HTML

Summary CSV

Gene Expression - Loupe Browser file

Gene Expression - Genome-aligned BAM

Gene Expression - Genome-aligned BAM index

Gene Expression - Sample barcodes

Gene Expression - Feature / cell matrix HDF5 (per-sample)

Gene Expression - Feature / cell matrix (per-sample)

Gene Expression - Per-molecule read information

Gene Expression - Feature Reference

Gene Expression - Clustering analysis

Gene Expression - CRISPR analysis

Gene Expression - Target Panel

VDJ Ig - AIRR rearrangement (TSV)

VDJ Ig - Cell Barcodes (JSON)

VDJ Ig - Clonotype info (CSV)

VDJ Ig - Concatenated Segments (BAM)

VDJ Ig - Concatenated Segments index (BAI)

VDJ Ig - Concatenated Segments (FASTA)

VDJ Ig - Concatenated Segments index (FAI)

VDJ Ig - Clonotype consensus annotations (CSV)

VDJ Ig - Clonotype consensus BAM

VDJ Ig - Clonotype consensus index BAI

VDJ Ig - Clonotype consensus FASTA

VDJ Ig - Clonotype consensus index FAI

VDJ Ig - Filtered contig annotations (CSV)

VDJ Ig - Filtered contig sequences FASTA

VDJ Ig - Filtered contig sequences FASTQ

VDJ Ig - All contig info (ProtoBuf)

VDJ Ig - Loupe V(D)J Browser file

VDJ TCR - AIRR rearrangement (TSV)

VDJ TCR - Cell Barcodes (JSON)

VDJ TCR - Clonotype info (CSV)

VDJ TCR - Concatenated Segments (BAM)

VDJ TCR - Concatenated Segments index (BAI)

VDJ TCR - Concatenated Segments (FASTA)

VDJ TCR - Concatenated Segments index (FAI)

VDJ TCR - Clonotype consensus annotations (CSV)

VDJ TCR - Clonotype consensus BAM

VDJ TCR - Clonotype consensus index BAI

VDJ TCR - Clonotype consensus FASTA

VDJ TCR - Clonotype consensus index FAI

VDJ TCR - Filtered contig annotations (CSV)

VDJ TCR - Filtered contig sequences FASTA

VDJ TCR - Filtered contig sequences FASTQ

VDJ TCR - All contig info (ProtoBuf)

VDJ TCR - Loupe V(D)J Browser file

Gene Expression - Antibody analysis

Gene Expression - Probe Set (CSV)

Gene Expression - Raw feature / cell matrix HDF5 (per-sample)

Gene Expression - Raw feature / cell matrix (per-sample)

Gene Expression - Raw probe barcode matrix (per-sample)

Cell Type Annotation Files

Summary

Sample Outputs

Chromium X Series

Universal 5' Gene Expression

Cell Ranger

10k Human PBMCs, Ultima Sequencing