We generated two in-house CITE-seq datasets of PBMCs from a healthy donor. Cells from both datasets are from the same aliquot of the sample, and thus are homogenous in nature. Cells were stained with the newly released TotalSeq-A panel (Human Universal Cocktail, V1.0) with a total of 154 unique cell surface antigens from BioLegend and are prepared using the 10x Genomics platform with Gel Bead Kit V2. Different antibody concentrations were used in each sample. In addition, we used cell hashing for sample multiplexing to eliminate batch effect between RNA data from each dataset. The prepared assay is subsequently sequenced on an Illumina HiSeq with a depth of 50 K reads per cell.
Gel bead kit v2
Manufactured by BioLegend
The Gel Bead Kit V2 is a laboratory equipment product designed for single-cell RNA sequencing. It is used to encapsulate individual cells within gel beads to facilitate high-throughput transcriptome analysis.
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Lab products found in correlation
2 protocols using gel bead kit v2
1
CITE-seq analysis of PBMC samples
2
CITE-seq Analysis of Human PBMC
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To further evaluate the validity of our method. We generated an in-house CITE-seq dataset of human PBMC from a healthy donor under IRB approval from the University of Pittsburgh. 1372 cells were stained with Totalseq-A from BioLegend and are prepared using the 10x Genomics platform with Gel Bead Kit V2. The prepared assay is subsequently sequenced on an Illumina Hiseq with a depth of 50K reads per cell. Cells in this dataset are measured for their surface marker abundance through CITE-seq (3 (link)). Ten surface markers are measured for every cell: CD3, CD4, CD8a, CD11c, CD14, CD16, CD19, CD56, CD127 and CD154. Cell Ranger 3.0 was used to process the data and generate UMI matrix for the downstream analysis.
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