mncfletcher/angel-gb-gemms

Code for the in silico analysis from Costa et al., 2021

A set of cell lines derived from a genetic murine glioblastoma model recapitulates molecular and morphological characteristics of human tumors

Barbara Costa*, Michael Fletcher, Pavle Boskovic, Ekaterina L. Ivanova, Tanja Eisemann, Sabrina Lohr, Lukas Bunse, Martin Löwer, Stefanie Burchard, Andrey Korshunov, Nadia Coltella, Melania Cusimano, Luigi Naldini, Hai-Kun Liu, Michael Platten, Bernhard Radlwimmer, Peter Angel*, Heike Peterziel

* co-corresponding authors [contact emails: b.costa [OR] p.angel [AT] dkfz-heidelberg.de]

Published online 2021-01-10: Cancers 2021, 13(2), 230; https://doi.org/10.3390/cancers13020230

Introduction

Kia ora! Welcome to the code repository, containing the RNAseq and WES analysis scripts for our paper.

All computational analyses were performed by Mike Fletcher [email: m.fletcher [AT] dkfz-heidelberg.de OR sci [AT] dismissed.net.nz]

For general enquiries, please contact the corresponding authors, Barbara and Peter (see above).

Analysis overview

A brief summary of how it all fits together:

For the RNAseq analysis:

1. RNAseq_Angel_GB_GEMMs_process.sh: as it says on the tin, do basic processing (STAR alignment to Gencode M2 transcriptome, featureCounts)
2. RNAseq_Angel_GB_GEMM_analysis.Rscript: takes the per-sample counts from featureCounts, and does the transcriptome characterisation, comparison to Wang 2017 GB signatures, aNSC signature activity

For the WES analysis:

1. WES_Angel_GB_GEMMs_process.sh and WES_SE_Angel_GB_GEMMs_process.sh: again, basic processing (bwa alignment), for paired or single end data respectively
2. WES_Angel_GB_GEMMs_SNV_mpileup.sh: use bcftools mpileup to check whether the Idh1/2 hotspot mutations appear in the genomic DNA
3. WES_Angel_GB_GEMM_CNV_calling_CNVkit.sh: call CNVs using CNV kit on WES data
4. WES_Angel_GB_GEMM_CNV_visualisation_excludeSegDupes.Rscript: visualise CNVkit CNV calls as Circos plots