Hi everyone!
We isolated and sequenced our nuclei, and performed hashing prior to sequencing by combining four samples in a single batch, with each sample being stained with a different TotalSeq B hashtag antibody. I am curious whether the 10X Cloud Analysis tool can support the demultiplex Cellranger pipeline for our specific case.
Thank you for your help.
The 10x Cloud Analysis platform is a suite of analysis tools for single-cell sequencing data generated using 10x Genomics technology. The TotalSeq B antibodies are oligonucleotide-conjugated antibodies designed for cell surface and intracellular protein analysis in combination with single-cell RNA sequencing (scRNA-seq) using the 10x Genomics Chromium platform.
TotalSeq B antibodies are designed to label cells for downstream analysis with scRNA-seq. While these antibodies can potentially label nuclei in addition to other cellular compartments, they are primarily optimized for labeling cell surface and intracellular proteins. Therefore, they may not be the most suitable reagents for nuclei staining in isolation.
However, the 10x Genomics platform supports additional assays, such as chromatin accessibility and gene expression, that can be used to analyze nuclei. For example, the ATAC-seq assay can be used to analyze chromatin accessibility, while the 10x Visium Spatial Gene Expression assay can be used to analyze gene expression in tissue sections.
In summary, while TotalSeq B antibodies are not optimized for nuclei staining in isolation, the 10x Genomics platform supports multiple assays that can be used to analyze nuclei and other cellular compartments.