DepleteX Single Cell RNA Boost Kit

Boost usable single cell RNA seq data with DepleteX™

Product Description

This product replaces CRISPRclean Single Cell RNA Boost Kit (KIT1018-JCG).

One problem faced by single cell RNA-seq methods is that greater than 90% of single cell RNA-seq dataset is noise and uninformative¹. While computational algorithms have evolved to parse out the true signal, commonly available microfluidic technologies enable only sparse sampling of RNAs from each cell, with many genes represented by a few sequencing reads. This limit is partially due to an abundance of biologically uninformative RNAs which dominate sequencing reads and limit detection of the moderately expressed transcripts that often drive biological differences between cell types.

¹ Qiu, P. Embracing the dropouts in single-cell RNA-seq analysis. Nat Commun 11, 1169 (2020).

DepleteX™ removes abundant and uninformative fragments 

The DepleteX Single Cell RNA Boost Kit removes abundant and uninformative fragments from human samples before sequencing, redistributing 50% sequencing clusters to informative reads that normally would be filtered out prior to secondary analysis. This kit leverages Cas9 depletion with an optimized guide set to remove ribosomal RNA, ribosomal and mitochondrial mRNA, non-transcriptomic reads, and highly expressed non-variable genes. With this new kit a separate tube for non-variable gene depletion content that can be included or excluded as needed is provided.

DepleteX Single Cell RNA Boost Kit gives you the ability to cut through the noise and maximize usable data in your single cell RNA sequencing.

• ~50% boost in reads useful for secondary analysis
• Validated for both short and long read sequencing
• Depletes ribosomal, mitochondrial, non-transcriptomic reads, and non-variable genes (optional) from single cell libraries
• Simple 3-step protocol

Fig.1. 100% increase in reads mapped to the transcriptome with DepleteX™ Single Cell RNA Boost Kit.

How it works

Fig.2. Simple 3-step protocol integrated into 10x Genomics® Chromium™ Next GEM Single Cell 3’ workflow

Specifications

Performance Data

Fig.3. 1.5x improvement in detection sensitivity with depletion. Boost in detection sensitivity of genes and UMIs per cell for depleted PBMC samples compared to undepleted sample.

Fig.4. Gain a deeper view of expression profiles. One additional cell type was identified in PBMC samples treated with CRISPRclean. UMAP plots of cell clusters with and without depletion using PBMC samples showed that depletion did not perturb cell type calls.