WTA 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 Protocols

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 Protocols

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

• BD Rhapsody™ System mRNA Whole Transcriptome Analysis (WTA) Library Preparation Protocol
  • This protocol provides instructions on creating a single cell whole transcriptome 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: 23-24117(03)
  • Revision date: 01/2025
• BD Rhapsody™ System mRNA Whole Transcriptome Analysis (WTA) and AbSeq Library Preparation Protocol
  • This protocol provides instructions on creating single cell whole transcriptome mRNA and AbSeq protein-detection libraries 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: 23-24118(03)
  • Revision date: 01/2025
• BD Rhapsody™ System mRNA Whole Transcriptome Analysis (WTA) and Sample Tag Library Preparation Protocol
  • This protocol provides instructions on creating single cell whole transcriptome mRNA and Sample Tag libraries 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: 23-24119(03)
  • Revision date: 01/2025
• BD Rhapsody™ System mRNA Whole Transcriptome Analysis (WTA), AbSeq, and Sample Tag Library Preparation Protocol
  • This protocol provides instructions on creating single-cell whole transcriptome mRNA, AbSeq, and Sample Tag libraries 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: 23-24120(03)
  • Revision date: 01/2025

Mitochondrial Depletion with Jumpcode Genomics kits

• This protocol provides guidelines on how to use the Deplete X kit from Jumpcode Genomics alongside the BD Rhapsody™ System mRNA Whole Transcriptome Analysis (WTA) Library Preparation Protocol for removing any undesired mitochondrial transcripts from the WTA library before sequencing.

For Data Analysis, please see the Bioinformatics Section

#23