All datasets

2k Transgenic HEL Mouse Splenocytes (BEAM-Ab)

Universal 5' Gene Expression dataset analyzed using Cell Ranger 7.1.0

Assess data quality
View summary metrics to assess data quality and more.
View summary
Visualize and explore data
Discover differentially expressed genes, visualize your favorite genes, and explore your data with our visualization software.

Learn about Chromium analysis

Splenocytes from transgenic mice that recognize Hen Egg Lysozyme (HEL) were labeled with a small antigen pool plus a negative control. Then they were sorted for CD19+/PE+ B cells as described in the Sample Prep User Guide for Reagent Assembly, Sample Labeling & Flow Sorting for Barcode Enabled Antigen Mapping (CG000595, Rev A).

Antigens:

  • SARS-TRI-S Wild Type (BEAM Conjugate 1): Biotinylated SARS-CoV-2 S protein, His, Avitag, Super stable trimer  is the ectodomain of SARS-CoV-2 S protein which contains AA Val 16 - Pro 1213.
  • Hen Egg Lysozyme (BEAM Conjugate 2): Biotinylated, Hen Egg Lysozyme
  • gp120 (BEAM Conjugate 3): Biotinylated HIV-1 [HIV-1/Clade B/C (CN54)] GP120 Protein, His,Avitag™
  • H5N1 (BEAM Conjugate 4): Biotinylated Influenza A [A/Hong Kong/483/97(H5N1)] Hemagglutinin 1 (HA1) Protein, Avitag™,His Tag
  • Negative control (BEAM Conjugate 5)

Gene Expression, Antigen Capture (BEAM-Ab), and VDJ-B amplified libraries were generated from the sorted cells as described in the Chromium Next GEM Single Cell 5' Reagent Kits User Guide (CG000591, Rev A) and sequenced on an Illumina NovaSeq 6000.

Paired-end, dual indexing libraries were sequenced to the following depths:

  • GEX: 87,699 mean reads per cell
  • Antigen Capture (BEAM-Ab): 9,316 mean reads per cell
  • VDJ-B: 21,892 mean reads per cell

Sequencing read configuration:

  • Read 1: 26 cycles (16 bp barcode, 10 bp UMI)
  • i5 index: 10 cycles (sample index)
  • i7 index: 10 cycles (sample index)
  • Read 2: 90 cycles (transcript)

Sequencing data were processed using Cell Ranger v7.1, with web summary and output files available in relevant tabs. A custom made mouse V(D)J reference was used as input. This reference differs from the pre-built mouse reference in the sequence of only one V(D)J gene. For more information, please contact support@10xgenomics.com.

  • Cells detected: 2,026
  • Median genes per cell: 1,856
  • Median UMIs per cell: 4,664

This dataset is licensed under the Creative Commons Attribution license.