QIAseq UPX 3' Transcriptome (96-M), Box2

The second-stage reagent module for an ultra-low input 3' RNA profiling workflow supplies library amplification, clean-up, and indexing components needed to convert amplified cDNA into Illumina-ready sequencing libraries. This QIAseq UPX 3' Transcriptome Box 2 kit targets the mid-throughput 96-sample format built for single-cell and low-input studies.

The chemistry combines a poly(A) capture strategy with cell- or well-specific barcodes, allowing multiplexed profiling of single cells, sorted targets, or rare populations without sequencing full transcript length. Each original mRNA molecule is tagged with a unique molecular identifier (UMI), correcting PCR duplication bias and supporting accurate transcript counting even from picogram input levels.

Researchers commonly apply this workflow to single-cell gene expression profiling, rare cell characterization, drug-response screens, and validation of bulk RNA-seq results. Generated libraries pair with standard Illumina sequencers such as NextSeq, NovaSeq, and MiSeq and can be pooled across plates for cost-efficient runs. Unique dual-indexed adapters are included to support unambiguous demultiplexing of a 96-reaction plate.

Key specifications: 96 reactions per box; an input range of 1 to 1000 cells or 10 pg to 10 ng total RNA; a recommended read configuration of 100 bp paired-end; libraries stored at -20 °C for long-term archiving after quantification. Reagents are supplied in single-use tubes and strip-tubes to limit freeze-thaw cycles and cross-contamination when processing a full plate.

QIAGEN's companion QIAseq UPX analysis pipeline handles UMI deduplication, well-barcode demultiplexing, and downstream count-matrix generation, letting laboratories move from lysed cells to a gene-by-cell expression table without writing custom scripts.