The data in this Zenodo entry corresponds to the data and results associated with the manuscript titled Cardiopulmonary bypass with deep hypothermic circulatory arrest results in organ-specific transcriptomic responses in pediatric swine and the Zenodo record.
To download file from Zenodo which will generate the results and data directories run
sh get_data.sh
or directly download the data from Zenodo, unzip the file and place the resulting directories here.
Once the Zenodo data is placed here, this repository will have the following structure
- data
- mapped_reads : generated by nf-core pipeline that is used in the analyses
- networks : data used to generate network clusters
- orthologs: data used to convert swine genes to human genes
- Sample info + gender with heart.csv : sample sheet describing labels of the samples
- results
- Make_DEG_Lists : results generated for the entire gene list (includes results for only looking at all up- or all down-regulated genes, which aren't included in the main manuscript)
- Make_Cluster : results of the network clustering analysis (includes results for only looking at all up- or all down-regulated genes, which aren't included in the main manuscript)
- nfcore_count_tables : count tables generated by the rnaseq pipeline run using nf-core
- src
- map_reads : script used to run nf-core pipeline
- analyses : script run to generate the results
- renv : contains information on R packages used
- requirements.txt : contains information on python packages used
Note: the names of the groups in these files are slightly different than in the manuscript
Controlnodrug = Control
CPBnodrug = CPB/DHCA
CPBLind = CPB/DHCA + Lin (Linrodostat analyses ended up not included in the published version of the manuscript)
The raw fastq files are deposited in GEO/SRA under GSE294547.
This study was funded by the National Institutes of Health/NHLBI R01HL156936