The genetic basis of cytoplasmic male sterility and fertility restoration in wheat

For dataset 1, the files included here are: experimental_design.xlsx — lists the samples and genotypes references — folder of fasta files containing reference transcripts for the respective genotypes (input to Salmon) quants — folder of quant.sf files containing nuclear/cytosolic transcript counts (output from Salmon) mt_quants — folder of quant.sf files containing mitochondrial transcript counts (output from Salmon) rnaseq.ipynb — Jupyter notebook (Python code) to reproduce Fig. 2b and Fig. S2 from the paper using the quants files (requires Python packages pandas, numpy, matplotlib, seaborn, sklearn and diffexpr (https://github.com/wckdouglas/diffexpr)) mt.ipynb — Jupyter notebook (Python code) to reproduce Figs. 2c and Fig. 2d from the paper using the mt_quants files For dataset 2, the files included here are: references — folder containing a fasta file containing reference transcripts (input to Salmon) RNASeq_quants.xlsx — table of read counts extracted from Salmon output mt_cov — folder of strand-specific read coverage files (generated by genomeCoverageBed from the bedtools2 package) Transgene_TPM.ipynb — Jupyter notebook (Python code) to reproduce Fig. 3c from the paper using the quants files mt_coverage.ipynb — Jupyter notebook (Python code) to reproduce Figures 5 and S5 from the paper using the mt_cov files The source data underlying Figs 2a, 3b-f, 4c-e, 6c, 7b and Supplementary Figs S3b, S4b-e, S6a and S7b-d are provided as a Source Data zip file.