Curated public datasets: import commands and configurations

Each curated single-cell dataset below ships with a tested import command and a pre-validated transformation configuration. For a given dataset, use its import command to load it into ODM, then run a transformation job with the configuration listed in that dataset's section.

The import commands use the odm-import-data CLI and upload the study and sample/library metadata alongside the H5AD attachment, ready for transformation. Replace <HOST>, <TOKEN>, and <TEMPLATE> with your ODM instance URL, API token, and template ID before running. Commands can be run independently and in any order.

Recommended template: Public dataset template

Because these configurations have been pre-validated against their datasets, you can skip the dry-run step when transforming the curated catalogue.

Two datasets (GSE192740 and GSE198623) contain multiple species and upload two H5AD files (human and mouse, or human and pig) within a single command.

For what the configuration fields mean, see the Configuration reference.

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Configuration index

Several datasets share an aggregated configuration. Each dataset's own section repeats the configuration that applies to it.

Configuration	Datasets
aggregated_config_1	HeartDiversityTucker10x · SCP1303 · GSE192740_human · GSE192740_mouse · GSE292928 · GSE148434
aggregated_config_2	GSE198623_human · GSE198623_pig
aggregated_config_3	GSE148073 · FibroticLiverWatsonMERFISH
GSE156793	GSE156793
GSE165045	GSE165045

---

HeartDiversityTucker10x

Configuration: aggregated_config_1

odm-import-data \
  --server <HOST> \
  --token <TOKEN> \
  --study https://bio-test-data.s3.us-east-1.amazonaws.com/demo_materials/non_onco/single_cell/cardiovascular_diseases/HeartDiversityTucker10x/study.tsv \
  --samples https://bio-test-data.s3.us-east-1.amazonaws.com/demo_materials/non_onco/single_cell/cardiovascular_diseases/HeartDiversityTucker10x/samples.tsv \
  --libraries https://bio-test-data.s3.us-east-1.amazonaws.com/demo_materials/non_onco/single_cell/cardiovascular_diseases/HeartDiversityTucker10x/libraries.tsv \
  -fl https://bio-test-data.s3.us-east-1.amazonaws.com/demo_materials/non_onco/single_cell/cardiovascular_diseases/HeartDiversityTucker10x/healthy_human_4chamber_map_unnormalized_V4.h5ad \
  -flm https://bio-test-data.s3.us-east-1.amazonaws.com/demo_materials/non_onco/single_cell/cardiovascular_diseases/HeartDiversityTucker10x/data.tsv \
  -dc 'Single-cell transcriptomics' \
  --template <TEMPLATE> \
  --allow-duplicates

---

SCP1303

Configuration: aggregated_config_1

odm-import-data \
  --server <HOST> \
  --token <TOKEN> \
  --study https://bio-test-data.s3.us-east-1.amazonaws.com/demo_materials/non_onco/single_cell/cardiovascular_diseases/SCP1303/study.tsv \
  --samples https://bio-test-data.s3.us-east-1.amazonaws.com/demo_materials/non_onco/single_cell/cardiovascular_diseases/SCP1303/samples.tsv \
  --libraries https://bio-test-data.s3.us-east-1.amazonaws.com/demo_materials/non_onco/single_cell/cardiovascular_diseases/SCP1303/libraries.tsv \
  -fl https://bio-test-data.s3.us-east-1.amazonaws.com/demo_materials/non_onco/single_cell/cardiovascular_diseases/SCP1303/human_dcm_hcm_scportal_03.17.2022.h5ad \
  -flm https://bio-test-data.s3.us-east-1.amazonaws.com/demo_materials/non_onco/single_cell/cardiovascular_diseases/SCP1303/data.tsv \
  -dc 'Single-cell transcriptomics' \
  --template <TEMPLATE> \
  --allow-duplicates

---

GSE156793

Configuration: GSE156793

odm-import-data \
  --server <HOST> \
  --token <TOKEN> \
  --study https://bio-test-data.s3.us-east-1.amazonaws.com/demo_materials/non_onco/single_cell/healthy_cell_atlases/GSE156793/study.tsv \
  --samples https://bio-test-data.s3.us-east-1.amazonaws.com/demo_materials/non_onco/single_cell/healthy_cell_atlases/GSE156793/samples.tsv \
  --libraries https://bio-test-data.s3.us-east-1.amazonaws.com/demo_materials/non_onco/single_cell/healthy_cell_atlases/GSE156793/libraries.tsv \
  -fl https://bio-test-data.s3.us-east-1.amazonaws.com/demo_materials/non_onco/single_cell/healthy_cell_atlases/GSE156793/GSE156793_all_organs_annotated_with_genes.h5ad \
  -flm https://bio-test-data.s3.us-east-1.amazonaws.com/demo_materials/non_onco/single_cell/healthy_cell_atlases/GSE156793/data.tsv \
  -dc 'Single-cell transcriptomics' \
  --template <TEMPLATE> \
  --allow-duplicates

---

FibroticLiverWatsonMERFISH

Configuration: aggregated_config_3

odm-import-data \
  --server <HOST> \
  --token <TOKEN> \
  --study https://bio-test-data.s3.us-east-1.amazonaws.com/demo_materials/non_onco/single_cell/inflammatory_diseases/FibroticLiverWatsonMERFISH/study.tsv \
  --samples https://bio-test-data.s3.us-east-1.amazonaws.com/demo_materials/non_onco/single_cell/inflammatory_diseases/FibroticLiverWatsonMERFISH/samples.tsv \
  --libraries https://bio-test-data.s3.us-east-1.amazonaws.com/demo_materials/non_onco/single_cell/inflammatory_diseases/FibroticLiverWatsonMERFISH/libraries.tsv \
  -fl https://bio-test-data.s3.us-east-1.amazonaws.com/demo_materials/non_onco/single_cell/inflammatory_diseases/FibroticLiverWatsonMERFISH/GSE210077_adata_healthy_diseased_nucseq_sparse.h5ad \
  -flm https://bio-test-data.s3.us-east-1.amazonaws.com/demo_materials/non_onco/single_cell/inflammatory_diseases/FibroticLiverWatsonMERFISH/data.tsv \
  -dc 'Single-cell transcriptomics' \
  --template <TEMPLATE> \
  --allow-duplicates

---

GSE165045

Configuration: GSE165045

odm-import-data \
  --server <HOST> \
  --token <TOKEN> \
  --study https://bio-test-data.s3.us-east-1.amazonaws.com/demo_materials/non_onco/single_cell/inflammatory_diseases/GSE165045/study.tsv \
  --samples https://bio-test-data.s3.us-east-1.amazonaws.com/demo_materials/non_onco/single_cell/inflammatory_diseases/GSE165045/samples.tsv \
  --libraries https://bio-test-data.s3.us-east-1.amazonaws.com/demo_materials/non_onco/single_cell/inflammatory_diseases/GSE165045/libraries.tsv \
  -fl https://bio-test-data.s3.us-east-1.amazonaws.com/demo_materials/non_onco/single_cell/inflammatory_diseases/GSE165045/GSE165045_merged_with_TCR.h5ad \
  -flm https://bio-test-data.s3.us-east-1.amazonaws.com/demo_materials/non_onco/single_cell/inflammatory_diseases/GSE165045/data.tsv \
  -dc 'Single-cell transcriptomics' \
  --template <TEMPLATE> \
  --allow-duplicates

---

GSE148073

Configuration: aggregated_config_3

odm-import-data \
  --server <HOST> \
  --token <TOKEN> \
  --study https://bio-test-data.s3.us-east-1.amazonaws.com/demo_materials/non_onco/single_cell/metabolic_diseases/GSE148073/study.tsv \
  --samples https://bio-test-data.s3.us-east-1.amazonaws.com/demo_materials/non_onco/single_cell/metabolic_diseases/GSE148073/samples.tsv \
  --libraries https://bio-test-data.s3.us-east-1.amazonaws.com/demo_materials/non_onco/single_cell/metabolic_diseases/GSE148073/libraries.tsv \
  -fl https://bio-test-data.s3.us-east-1.amazonaws.com/demo_materials/non_onco/single_cell/metabolic_diseases/GSE148073/GSE148073_merged_data_new.h5ad \
  -flm https://bio-test-data.s3.us-east-1.amazonaws.com/demo_materials/non_onco/single_cell/metabolic_diseases/GSE148073/data.tsv \
  -dc 'Single-cell transcriptomics' \
  --template <TEMPLATE> \
  --allow-duplicates

---

GSE192740 (human + mouse)

Configuration: aggregated_config_1

odm-import-data \
  --server <HOST> \
  --token <TOKEN> \
  --study https://bio-test-data.s3.us-east-1.amazonaws.com/demo_materials/non_onco/single_cell/metabolic_diseases/GSE192740/study.tsv \
  --samples https://bio-test-data.s3.us-east-1.amazonaws.com/demo_materials/non_onco/single_cell/metabolic_diseases/GSE192740/samples.tsv \
  --libraries https://bio-test-data.s3.us-east-1.amazonaws.com/demo_materials/non_onco/single_cell/metabolic_diseases/GSE192740/libraries.tsv \
  -fl https://bio-test-data.s3.us-east-1.amazonaws.com/demo_materials/non_onco/single_cell/metabolic_diseases/GSE192740/GSE192740_human_combined_sparse.h5ad \
  -flm https://bio-test-data.s3.us-east-1.amazonaws.com/demo_materials/non_onco/single_cell/metabolic_diseases/GSE192740/data_human.tsv \
  -dc 'Single-cell transcriptomics' \
  -fl https://bio-test-data.s3.us-east-1.amazonaws.com/demo_materials/non_onco/single_cell/metabolic_diseases/GSE192740/GSE192740_mouse_combined_sparse.h5ad \
  -flm https://bio-test-data.s3.us-east-1.amazonaws.com/demo_materials/non_onco/single_cell/metabolic_diseases/GSE192740/data_mouse.tsv \
  -dc 'Single-cell transcriptomics' \
  --template <TEMPLATE> \
  --allow-duplicates

---

GSE198623 (human + pig)

Configuration: aggregated_config_2

odm-import-data \
  --server <HOST> \
  --token <TOKEN> \
  --study https://bio-test-data.s3.us-east-1.amazonaws.com/demo_materials/non_onco/single_cell/metabolic_diseases/GSE198623/study.tsv \
  --samples https://bio-test-data.s3.us-east-1.amazonaws.com/demo_materials/non_onco/single_cell/metabolic_diseases/GSE198623/samples.tsv \
  --libraries https://bio-test-data.s3.us-east-1.amazonaws.com/demo_materials/non_onco/single_cell/metabolic_diseases/GSE198623/libraries.tsv \
  -fl https://bio-test-data.s3.us-east-1.amazonaws.com/demo_materials/non_onco/single_cell/metabolic_diseases/GSE198623/GSE198623_human_processed.h5ad \
  -flm https://bio-test-data.s3.us-east-1.amazonaws.com/demo_materials/non_onco/single_cell/metabolic_diseases/GSE198623/data_human.tsv \
  -dc 'Single-cell transcriptomics' \
  -fl https://bio-test-data.s3.us-east-1.amazonaws.com/demo_materials/non_onco/single_cell/metabolic_diseases/GSE198623/GSE198623_pig_processed.h5ad \
  -flm https://bio-test-data.s3.us-east-1.amazonaws.com/demo_materials/non_onco/single_cell/metabolic_diseases/GSE198623/data_pig.tsv \
  -dc 'Single-cell transcriptomics' \
  --template <TEMPLATE> \
  --allow-duplicates

---

GSE292928

Configuration: aggregated_config_1

odm-import-data \
  --server <HOST> \
  --token <TOKEN> \
  --study https://bio-test-data.s3.us-east-1.amazonaws.com/demo_materials/non_onco/single_cell/metabolic_diseases/GSE292928/study.tsv \
  --samples https://bio-test-data.s3.us-east-1.amazonaws.com/demo_materials/non_onco/single_cell/metabolic_diseases/GSE292928/samples.tsv \
  --libraries https://bio-test-data.s3.us-east-1.amazonaws.com/demo_materials/non_onco/single_cell/metabolic_diseases/GSE292928/libraries.tsv \
  -fl https://bio-test-data.s3.us-east-1.amazonaws.com/demo_materials/non_onco/single_cell/metabolic_diseases/GSE292928/GSE292928_GEX_only_cellbender_sparse.h5ad \
  -flm https://bio-test-data.s3.us-east-1.amazonaws.com/demo_materials/non_onco/single_cell/metabolic_diseases/GSE292928/data.tsv \
  -dc 'Single-cell transcriptomics' \
  --template <TEMPLATE> \
  --allow-duplicates

---

GSE148434

Configuration: aggregated_config_1

odm-import-data \
  --server <HOST> \
  --token <TOKEN> \
  --study https://bio-test-data.s3.us-east-1.amazonaws.com/demo_materials/non_onco/single_cell/neurodegenerative_diseases/GSE148434/study.tsv \
  --samples https://bio-test-data.s3.us-east-1.amazonaws.com/demo_materials/non_onco/single_cell/neurodegenerative_diseases/GSE148434/samples.tsv \
  --libraries https://bio-test-data.s3.us-east-1.amazonaws.com/demo_materials/non_onco/single_cell/neurodegenerative_diseases/GSE148434/libraries.tsv \
  -fl https://bio-test-data.s3.us-east-1.amazonaws.com/demo_materials/non_onco/single_cell/neurodegenerative_diseases/GSE148434/GSE148434_merged_data.h5ad \
  -flm https://bio-test-data.s3.us-east-1.amazonaws.com/demo_materials/non_onco/single_cell/neurodegenerative_diseases/GSE148434/data.tsv \
  -dc 'Single-cell transcriptomics' \
  --template <TEMPLATE> \
  --allow-duplicates