text.skipToContent text.skipToNavigation

QIAseq UPX 3’ Targeted RNA Panels

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

Buy Products

Cat No./ID: 333041
QIAseq UPX 3' Targeted RNA Panel (96)
Go to GeneGlobe
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)

Cat No./ID: 333042
QIAseq UPX 3' Targeted RNA Panel (96-M)
Go to GeneGlobe
For 3' targeted RNA sequencing of 4 x 96 cells, cell pellets or ultralow-input RNA samples: Kit contains a 96-well plate with 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 384 samples (up to 1000 genes per sample)
Cat No./ID: 333043
QIAseq UPX 3' Targeted RNA Panel (384)
Go to GeneGlobe
For 3' targeted RNA sequencing of 384 cells, cell pellets or ultralow input RNA samples: Kit contains RT reaction-ready 384-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 384 samples (up to 1000 genes per sample)

Cat No./ID: 333044
QIAseq UPX 3' Targeted RNA 12 index (48)
R$2,357.00
Order Product
Sample indices for multiplexing up to 12 x 96 or 12 x 384 plates per lane (total of 48 plates can be indexed)
Cat No./ID: 333051
QIAseq UPX 3' Targeted 96 Index A (384)
Sample index for multiplexing up to 96 x 96 or 96 x 384 plates per lane (total of 384 plates can be indexed)
Cat No./ID: 333052
QIAseq UPX 3' Targeted 96 index B (384)

Sample index for multiplexing up to 96 x 96 or 96 x 384 plates per lane (total of 384 plates can be indexed)
 

Cat No./ID: 333053
QIAseq UPX 3' Targeted 96 index C (384)

Sample index for multiplexing up to 96 x 96 or 96 x 384 plates per lane (total of 384 plates can be indexed)

Cat No./ID: 333054
QIAseq UPX 3' Targeted 96 index D (384)
Sample index for multiplexing up to 96 x 96 or 96 x 384 plates per lane (total of 384 plates can be indexed)
QIAseq UPX 3’ Targeted RNA Panels are intended for molecular biology applications. These products are not intended for the diagnosis, prevention, or treatment of a disease.

Product Details

0
Principle of the QIAseq UPX 3' Targeted RNA Panel Workflow.
1
QIAseq UPX 3’ Targeted RNA Panel Workflow Exhibits Strong reproducibility at Ultra-low Input RNA Amounts.
The QIAseq UPX 3’ Targeted RNA Panel Library Kit was used to construct libraries from 380 replicates of 20 pg Human Universal total RNA aliquots. Reverse transcription was performed on each aliquot. Following this, the 380 aliquots were combined into one tube, since each cDNA is tagged with a unique Cell/Well ID. Subsequent targeted amplification and library construction steps were performed in a single tube and sequencing was performed on a MiSeq. QIAseq UPX 3' Analysis software was used for primary results mapping and deconvolution of the Cell/Well IDs. The average raw (non-normalized) Unique Molecular Index (UMI) counts and standard deviation for each gene are plotted demonstrating the strong reproducibility of QIAseq UPX at ultra-low input RNA amounts.
2
QIAseq UPX 3’ Targeted RNA Panel Workflow Exhibits Strong Linearity from 10 pg to 1 ng Total RNA.
The QIAseq UPX 3’ Targeted RNA Panel Library Kit was used to construct libraries from 10 pg, 100 pg and 1 ng aliquots of Human Universal total RNA. Reverse transcription was performed on six aliquots of each RNA amount (18 total aliquots). Following this, the 18 aliquots were combined into one tube, since each cDNA is tagged with a unique Cell/Well ID. Subsequent targeted amplification and library construction steps were performed in a single tube and sequencing was performed on a MiSeq. QIAseq UPX 3’ Analysis software was used for primary results mapping and deconvolution of the Cell/Well IDs. The average Unique Molecular Index (UMI) counts for each gene are plotted for 10 pg vs 100 pg (A) and 100 pg vs 1 ng (B) demonstrating the strong linearity of QIAseq UPX for both single cell and ultra-low input applications.
3
Sample to Insight Workflow of QIAseq UPX 3’ Targeted RNA Enables Identification of Cells Isolated with the QIAscout System.
The QIAseq UPX 3' Targeted RNA Panel Library Kit was used to construct targeted libraries from 96 cells isolated with the QIAscout System (32 cells were isolated from each cell line). Reverse transcription was performed on individual wells. Following this, the entire plate was combined into one tube, since each cDNA is tagged with a unique Cell ID. Subsequent targeted amplification and library construction steps were performed in a single tube and sequencing was performed on a MiSeq (two plates per sequencing run). QIAseq UPX 3' Analysis software was used for primary analysis and mapping and single cell secondary analysis. The TSNE Plot (included in the QIAseq UPX software) provides a visual representation of the data from each cell, where the expression of genes is reduced to a low dimensional space. The clustering of the cells, based on the K-means method, is depicted by colors of the cells. For this experiment, three clusters of cells were observed. This matches the expected results, as three different cell types were originally collected.
4
Sample to Insight Workflow of QIAseq UPX 3’ Targeted RNA Enables Identification of Cell Subtype Clusters.
The QIAseq UPX 3' Targeted RNA Panel Library Kit was used to construct targeted libraries from 96 cells sorted with FACS. Reverse transcription was performed on individual wells. Following this, the entire plate was combined into one tube, since each cDNA is tagged with a unique Cell ID. subsequent targeted amplification and library construction steps were performed in a single tube and sequencing was performed on a MiSeq (two plates per sequencing run). The QIAseq UPX 3' Analysis software was used for primary analysis and mapping and single cell secondary analysis. The TSNE Plot (included in the QIAseq UPX software) provides a visual representation of the data from each cell, where the expression of genes is reduced to a low dimensional space. The clustering of the cells, based on the K-means method, is depicted by colors of the cells. For this experiment, two clusters of cells were observed, in line with the expected results based on the initial sorting parameters.
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").
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").
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

Product Resources

You are not authorized to download the resource

Quick-Start Protocols (2)
fragment fix placeholder