RNA-seq Bioinformatics

Introduction to bioinformatics for RNA sequence analysis

scRNA-seq Data

Obtain RNA-seq test data.

The data that will be used to demonstrate scRNA analysis in this module has been published by Freshour et al. 2023. If you use this data in your own benchmarking, tool development, or research please cite this article. The complete raw sequence dataset can be obtained from SRA at accession: PRJNA934380.


Model system

The full details can be found in the publication but briefly these data are generated from a murine bladder cancer model system with the following characteristics:

Experimental details

Briefly, the experimental details are depicted below and summarized briefly here.


Data generation

The method and types of data generation are depicted below and summarized briefly here.


Description of samples/replicates and QC reports

In the following demonstration analyses we will focus on a simplified comparison of two biological conditions: treatment with checkpoint (“ICB”) or treatment with ICB after depletion of CD4 cells in the mice (“ICB-dT”). For each of these two conditions we will have three replicates (of five total reported in the publication).

List of replicates with labels and links to CellRanger 7.0.0 multi QC reports:

QC report discussion

Using the report for Rep1_ICB as an example, explore and discuss the following points:

Input files for the demonstration analysis

We will not be running Cell Ranger ourselves and will instead be starting the scRNA analysis in R using matrix files from Cell Ranger (cellrange multi to be precise) and a few other input files briefly described here:

Loupe browser demonstration for preliminary exploration of the MCB6C

Briefly explore the MCB6C data using the 10X Loupe browser. Use the following two samples as examples:

Input data files
Sample GEX Cloupe TCR Vloupe BCR Vloupe
REP3_ICB: Rep3_ICB GEX cloupe Rep3_ICB TCR vloupe Rep3_ICB BCR vloupe
REP3_ICBdT: Rep3_ICBdT GEX cloupe Rep3_ICBdT TCR vloupe Rep3_ICBdT BCR vloupe



Work through the following very basic intro to this tool with the following steps: