In this project, I was the bioinformatician consultant under the Genomics and Data Analytics Core for a scientific project (see Project Description). Here, I analysed single-cell RNA-sequencing datasets of mouse bladder tumors generated from the Parse Evercode Whole Transcriptome Mini kit. The writeup for the project at various stages of analysis can be found in the reports/ folder. Results were used for this journal submission abstract submission.
The results of the analysis was used to generate figure 3 of the Publication, and supplementary figures S1, S2, S3 and main figure 3.
Bladder tumors were implanted orthotopically into 3 WT and 4 GSTT2-KO mice (7 samples) at 3-4 months of age and then treated with 4 instillations of M. bovis BCG, following which the bladders were harvested and isolated as single cells for scRNA-seq.
The 2 scRNAseq sublibraries were prepared via the Parse Biosciences Evercode Whole Transcriptome Mini kit, which consists of a total of 12 wells per kit. The sample loading specification table is stored in sampleLoadingTable.txt. The output logs from running the various steps of the Parse biosciences v1.0.4p pipeline are kept
in the splitpipe_logs folder. Old reports submitted to the investigators are
placed in reports/.
Following the generation of the cells x gene count matrix, the data was analysed in R using the Seurat package. Standard downstream Seurat analyses was conducted, including dimensional reduction and clustering, marker gene identification, manual cell type annotation and pathway enrichment analysis. Scripts for differential abundance (DA) analysis and differential state analysis are included alongside the aforementioned analysis in scripts/, which were run in a previous round of analysis.
s3://parse-biosciences-mugdha On Biodebian, the files are stored at: /media/gedac/kane/projects/parse-bladder-scrnaseq
The files in this repository are also stored in an S3 bucket: s3://parse-scrnaseq-bladder/. The raw and processed data files are kept in the
data/ folder. R objects are kept in the rds/ folder.
PhD student: Mugdha Vijay Patwardhan Principal Investigator: Ratha Mahendran Bioinformatician: Toh Qin Kane
Approximately 15h (extensive amount of work, approx 80+h since October 2022,was performed as a gesture of goodwill, prior to an official consulting model being put in place).
Patwardhan, M. V., Kane, T. Q., Chiong, E., Rahmat, J. N., & Mahendran, R. (2024). Loss of Glutathione-S-Transferase Theta 2 (GSTT2) Modulates the Tumor Microenvironment and Response to BCG Immunotherapy in a Murine Orthotopic Model of Bladder Cancer. International journal of molecular sciences, 25(24), 13296. https://doi.org/10.3390/ijms252413296