Integrated analysis of TKI-treated and untreated PBMCs - gene expression & vdj libraries

Question

[divya.samuel]

My experiment is scRNA seq + VDJ analysis from the same samples using 10X Genomics kits. I want to compare the top differentially expressed genes & look for clonotype expansions in PBMCs isolated from timepoint 0 & timepoints 1 from 3 patients. So I have 6 samples: 3 samples per patient & 18 libraries: TCR, BCR, gene expression = 3 libraries per sample.

1. Is the integrated analysis tutorial the approach for my experiment?
2. What should my metadata look like when I integrate multiple datasets mentioned above?
3. How is integration different from merging?

Answer 1

[swbarnes2]

For 10x samples, the typical way to integrate samples is to use cellranger aggregate to combine all the gene expression data into one aggregated file. You can examine the cLoupe file from the gene expression samples in the Loupe Cell browser. You can also import vloupe files made by cellranger vdj into the cell browser Loupe program, and it will combine all the gene expression data together.

You can also import cLoupe files into the vdj Loupe viewer, though I think al it will keep track of is clustering, not gene expression.