QIAseq UPX 3’ Targeted RNA Panels

For ultraplex (UPX) gene expression analysis using 3' RNA-seq from single cells and low-input samples

Features

  • Target up to 1000 genes using a cost-effective, time-saving single-tube library prep
  • LNA-enhanced chemistry for increased accuracy, specificity and sensitivity
  • UMIs eliminate library amplification bias for accurate gene expression
  • Cell tagging and sample indexing enables simultaneous sequencing of up to 147,456 targeted libraries
  • Includes cloud-based read alignment and single-cell or low-input analysis
QIAseq UPX 3' Targeted RNA Panel (96)

Cat. No. / ID: 333041

For 3' targeted RNA sequencing of 96 cells, cell pellets or ultralow-input RNA samples: Kit contains a breakable 96-well plate with lyophilyzed reagents for cell lysis, cDNA synthesis with Unique Molecular Indexing along with a gene-specific panel for 3' RNA-seq library construction; for a total of 96 samples (up to 1000 genes per sample)
PanelIndex
QIAseq UPX 3' Targeted RNA Panel
QIAseq UPX 3' Targeted 96 index
QIAseq UPX 3' Targeted RNA 12 index
Samples
96
4 x 96
384
 CONFIGURE AT GeneGlobe

Product Details

QIAseq UPX 3' Targeted RNA Panels use unique molecular index (UMIs) and ultraplex (UPX) technology to enable accurate gene expression using 3' RNA-seq from single cells (1–1000), cell pellets and previously isolated total RNA (1 pg to 10 ng). Use our custom builder to design your custom panel for up to 1000 genes. UPX technology allows up to 384 plates of 384 samples (147,456 total samples) to be multiplexed together at one time. QIAseq UPX 3' Targeted Panels are available for 96 or 384 samples. For processing less than 96 samples at a time, use QIAseq UPX 3' Targeted RNA Panel (96) (cat. no. 333041), which is supplied with a breakable plate enabling processing of as few as 24 samples at one time for sequencing. The QIAseq UPX 3' Targeted RNA Panel (96-M) (cat. no. 333042) is for processing 96 samples in parallel 4 times (384 samples). The QIAseq UPX 3' Targeted RNA Panel (384) (cat. no. 333043) is for processing 384 samples simultaneously. QIAseq UPX 3' Targeted RNA Panels are only compatible with QIAseq UPX Targeted RNA Indices, which must be used during library construction for correct indexing.

Performance

Strong reproducibility at ultra-low input RNA amounts
Due to its LNA-enhanced chemistry, the QIAseq UPX 3’ Targeted RNA Panel workflow exhibits strong reproducibility at ultra-low input RNA amounts (see figure " QIAseq UPX 3’ Targeted RNA Panel workflow exhibits strong reproducibility at ultra-low input RNA amounts").

Strong linearity from 10 pg to 1 ng
The QIAseq UPX 3’ Targeted RNA Panel workflow shows strong linearity from 10 pg to 1 ng (see figure " QIAseq UPX 3’ Targeted RNA Panel workflow exhibits strong linearity from 10 pg to 1 ng of total RNA").

3' RNA-seq from single cells
QIAseq UPX 3' Targeted RNA Panels enable accurate gene expression using 3' RNA-seq from single cells (see figure " Sample to Insight Workflow of QIAseq UPX 3’ Targeted RNA Enables Identification of Cells Isolated with the QIAscout System"). The kit also enables sucessful identification of cell subtype clusters (see figure " Sample to Insight Workflow of QIAseq UPX 3’ Targeted RNA Enables Identification of Cell Subtype Clusters").
See figures

Principle

QIAseq UPX 3' Targeted RNA Panels enable high-throughput next-generation sequencing (NGS) of up to 1000 polyadenylated RNAs on Illumina sequencers. These panels are intended for library construction and analysis of single cells, cell pellets and ultralow amounts of purified RNA. Single cells or isolated RNA are reverse transcribed and each RNA molecule is given a Unique Molecular Index (UMI) and well-specific IDs are assigned (up to 384 wells; Cell IDs). Following reverse transcription, all cDNAs are combined, enabling simplified library construction steps to be performed in a single tube (see figure " Principle of the QIAseq UPX 3' Targeted RNA Panel Workflow").
See figures

Procedure

Innovative, optimized workflow
QIAseq UPX 3' Targeted RNA Panels enable Sample to Insight, high-throughput next-generation sequencing (NGS) of polyadenylated RNAs from single cells on Illumina NGS instruments. In addition, QIAseq UPX is intended for library construction and analysis of cell pellets (up to 100 cells) and purified RNA (10 pg to 1 ng). QIAseq UPX presents an innovative advantage in that, during reverse transcription, each cell is tagged with a unique ID (up to 384 different IDs) and each RNA molecule is tagged with a unique index. Following reverse transcription, all cDNAs are combined, which enables all subsequent library construction steps to be performed in a single tube. This prevents sample mixup, saves substantial time and dramatically reduces library prep costs. Target enrichment technology further enhances the power of QIAseq UPX by enabling users to sequence specific genes of interest, which effectively increases sequencing depth and sample throughput, while minimizing cost. Universal library amplification then assigns up to 384 different sample IDs. Together, the combination of Cell IDs and the Sample IDs enables up to 147,456 targeted libraries to be sequenced together. Ultimately, QIAseq UPX data analysis enables primary mapping, single-cell clustering analysis and differential expression analysis. Collectively, the Sample to Insight workflow of QIAseq UPX defines a new generation of high-throughput NGS technologies.

Applications

  • High-throughput screening applications (e.g., toxicology research)
  • Single-cell analysis
  • Differential gene expression analysis

Supporting data and figures

Resources

Quick-Start Protocols (2)
Part 2: Single primer extension
Part 1: Cell lysis, reverse transcription
Next Generation Sequencing (1)
Kit Handbooks (1)
Supplementary Protocols (1)