Supplementary data for human Y-chromosome gene expression analysis

Processed data for:

AK Godfrey, S Naqvi, L Chmátal, JM Chick, RN Mitchell, SP Gygi, H Skaletsky, DC Page. Quantitative analysis of Y-chromosome gene expression across 36 human tissues. Genome Res (2020).

The following six files are provided for reference and for use in future analyses.

(1) gencode.v24.annotation.basic_ccds_nopar.gtf.gz — transcriptome annotation used in analyses

(2) gtex.ksto.gen24c.prefilt_pass1.genes.est_counts.txt.gz — genes x samples matrix containing estimated count values output by kallisto for all samples passing initial set of metadata-based filters.

(3) gtex.ksto.gen24c.prefilt_pass1.pcgenes.tpm.txt.gz — protein-coding genes x samples matrix containing TPM values output by kallisto for all samples passing initial set of metadata-based filters. 

(4) gtex.ksto.gen24c.prefilt_pass1.postfilt_pass.pcgenes.tpm.txt.gz — protein-coding genes x samples matrix containing TPM values output by kallisto for samples passing initial metadata-based filters and expression-outlier filters.

(5) gtex.ksto.gen24c.prefilt_pass1.postfilt_pass.pcgenes.adj_tpm.txt.gz — protein-coding genes x samples matrix (based on file #4 above) containing TPM values adjusted for RIN, ischemic time, and intronic-read mapping rate.

(6) gtex_metadata_subset.txt — sample/donor metadata

The remaining 24 files contain the input data required to replicate analyses in the manuscript, as detailed at https://github.com/akg8/MSY-expression. HDF5 (`.h5`) files contain individual pandas DataFrame objects with the key `df`. These files can be downloaded individually, or they can be downloaded all at once by downloading the file msy_expression.all_input_data.zip (recommended).

---

Version history:

• Version 1 contained just the six listed files above.
• In Version 2, the remaining 24 files needed for reproducing analyses were added. In addition, gtex_metadata_subset.txt was updated with the previously missing column `SEX`.
• In Version 3, a single zipped file msy_expression.all_input_data.zip was added so that all input data for re-analysis can be downloaded more conveniently.