This dataset comes from a 2018 publication (Lee et. al., 2018) that created several bladder PDO lines from xenografts in mice and performed sequencing and drug experiments.
Sample information can be found on Synapse here.
This study had copy number variation, RNA-seq and mutation data that was included.
Copy number data is available at this synapse link. Mutation data is available at this synapse link. RNA-Seq data was acquired from GEO, we used the 'GSE1039990_Normalized_counts.txt.gz' table available on GEO GSE103990.
For these data, we had complete drug dose-response data to recalculate curves, available on Synapse in the Lee Bladder PDO Datasets folder.
python3 00_createbladderSampleFile.py --token $SYNAPSE_AUTH_TOKEN -p prevSamples
# for mutation data (-m)
python3 01_createbladderOmicsFiles.py --token $SYNAPSE_AUTH_TOKEN -s curSamples -g genes.csv -m
# for expressiondata (-e)
python3 01_createbladderOmicsFiles.py --token $SYNAPSE_AUTH_TOKEN -s curSamples -g genes.csv -e
# for copynumber (-c)
python3 01_createbladderOmicsFiles.py --token $SYNAPSE_AUTH_TOKEN -s curSamples -g genes.csv -c
# for running locally (from coderbuild directory):
python3 -m bladder.02_createbladderDrugsFile --token $SYNAPSE_AUTH_TOKEN -d prevDrugFilePath -o ./bladder/bladder_drugs.tsv
# for running in Docker as part of full build
python3 02_createbladderDrugsFile.py --token $SYNAPSE_AUTH_TOKEN -d prevDrugFilePath -o /tmp/bladder_drugs.tsv
# for running locally (from coderbuild directory):
python3 utils/build_drug_desc.py --drugtable ./bladder/bladder_drugs.tsv --desctable ./bladder/bladder_drug_descriptors.tsv.gz
# for running in docker as part of full build
python3 build_drug_desc.py --drugtable /tmp/bladder_drugs.tsv --desctable /tmp/bladder_drug_descriptors.tsv.gz
python3 03_createbladderExperimentFile.py --token $SYNAPSE_AUTH_TOKEN --drugfile curDrugFile --curSampleFile curSampleFile --output /tmp/bladder_doserep.tsv
python3 fit_curve.py --input /tmp/bladder_doserep.tsv --output /tmp/bladder_experiments.tsv