10x Genomics Support/Single Cell Multiome ATAC + Gene Expression/Documentation/Sequencing/

Interpreting Intronic and Antisense Reads in 10x Genomics Single Cell Gene Expression Data

  • CG000376_TechNote_Antisense_Intronic Reads_SingleCellGeneExpression_RevA.pdf

    Technical Note, CG000376

    CG000376_TechNote_Antisense_Intronic Reads_SingleCellGeneExpression_RevA.pdf

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Chromium Single Cell Gene Expression products enable the profiling of tens of thousands of cells, enhancing the understanding of complex biological systems and diseases. Analysis of whole transcriptome data derived from Chromium Single Cell 3’ and 5’ Gene Expression libraries provides key cellular insights and interpretation of these data may be impacted if intronic and antisense reads are included in the analysis. This Technical Note discusses potential mechanisms that can result in intronic and/or antisense read generation in Chromium Single Cell Gene Expression assays. The document also analyzes data supporting each mechanism and elaborates on the overall impact of intronic and antisense reads on gene expression data analysis and interpretation.


  • Chromium Single Cell 3’ Gene Expression (v3, v3.1, v3.1 Dual Index, HT v3.1, LT v3.1)
  • Chromium Single Cell 5’ Gene Expression (v1, v1.1, v2, HT v2)
  • Chromium Single Cell Multiome ATAC + Gene Expression (GEX libraries only)
Document Type
Technical Note

Last Modified
August 9, 2021