Targeted Gene Expression Analysis Protocols

For Single Cell Preparation and Preservation Protocols, see Sample Prep and Preservation Section 

For Cell Labelling Protocols, see BD® AbSeq Intracellular and Cell Surface Protein Profiling Section or the BD® Single-Cell Multiplexing Kit (SMK and Flex SMK) section

Single Cell Capture and cDNA Synthesis

Single lane cartridge

• Without scanner : Single-Cell Capture and cDNA Synthesis with the BD Rhapsody™ Express Single-Cell Analysis System
  • This protocol describes cell loading in the BD Rhapsody™ Cartridge and single-cell capture with the BD Rhapsody™ Express Single-Cell Analysis system.
  • Doc ID: 23-22952(02)
  • Revision date: 11/2022
• With scanner : Single-Cell Capture and cDNA Synthesis with the BD Rhapsody™ Single-Cell Analysis System
  • This protocol describes cell loading in the BD Rhapsody™ Cartridge and single-cell capture with the BD Rhapsody™ Single-Cell Analysis System with the BD Rhapsody™ Scanner.
  • Doc ID: 23-22951(02)
  • Revision date: 11/2022

8 lane High Throughput cartridge

• With Scanner : BD Rhapsody™ HT Single-Cell Analysis System Single-Cell Capture and cDNA Synthesis
  • This protocol describes cell loading in the BD Rhapsody™ 8-Lane Cartridge and single-cell capture with the BD Rhapsody™ HT Single-Cell Analysis System.
  • Doc ID: 23-24252(03)
  • Revision date: 04/2025
• Without Scanner : BD Rhapsody™ HT Xpress System Single-Cell Capture and cDNA Synthesis
  • This protocol describes cell loading in the BD Rhapsody™ 8-Lane Cartridge and single-cell capture with the BD Rhapsody™ HT Xpress System.
  • Doc ID: 23-24253(03)
  • Revision date: 04/2025

Sequencing Library Preparation

The following protocols are designed for use with the Enhanced Cartridge Reagent Kit (catalog number 664887 or 667052), do not use with v1 beads or older bead versions.

• BD Rhapsody™ System mRNA Targeted Library Preparation Protocol
  • This protocol provides instructions on creating a single cell mRNA library after cell capture on the BD Rhapsody™ Single-Cell Analysis system or the BD Rhapsody™ Express Single-Cell Analysis system for sequencing on Illumina sequencers.
  • Doc ID: 23-24121(03)
  • Revision date: 01/2025
• BD Rhapsody™ System mRNA Targeted and Sample Tag Library Preparation Protocol
  • This protocol provides instructions on creating single cell mRNA and Sample Tag libraries with the BD RhapsodyTM Single-Cell Analysis system or the BD RhapsodyTM Express Single-Cell Analysis system for sequencing on Illumina sequencers.
  • Doc ID: 23-24122(03)
  • Revision date: 01/2025
• BD Rhapsody™ System mRNA Targeted and BD® AbSeq Library Preparation Protocol
  • This protocol provides instructions on creating mRNA and BD® AbSeq single cell libraries with the BD Rhapsody™ Single-Cell Analysis system or the BD Rhapsody™ Express Single-Cell Analysis system for sequencing on Illumina sequencers.
  • Doc ID: 23-24123(03)
  • Revision date: 01/2025
• BD Rhapsody™ System mRNA Targeted, Sample Tag, and BD® AbSeq Library Preparation Protocol
  • This protocol provides instructions on creating single cell mRNA, Sample Tag, and BD® AbSeq libraries with the BD Rhapsody™ Single-Cell Analysis system or the BD Rhapsody™ Express Single-Cell Analysis system for sequencing on Illumina sequencers.
  • Doc ID: 23-24124(03)
  • Revision date: 01/2025

For Data Analysis, please see the Bioinformatics Section

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