Upload public repository-specific manifests
Browse files- manifest/GENE_TARGET_MAPPING.tsv +0 -0
- manifest/RELEASE_FILES.tsv +266 -0
- manifest/SCVI_RUNS.tsv +0 -0
- manifest/SOURCE_STUDY_PROVENANCE.tsv +17 -0
- manifest/STUDY_SUMMARY.tsv +17 -0
- manifest/TRAINING_UNITS.tsv +0 -0
- manifest/UPLOAD_MANIFEST.tsv +0 -0
manifest/GENE_TARGET_MAPPING.tsv
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source study_id publication_doi pmid primary_data_accession primary_data_url source_collection_release source_collection_url collection_data_license license_evidence_url redistribution_status redistribution_risk required_release_action notes
|
| 2 |
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XCell XAtlasOrion2025 10.1101/2025.06.11.659105 not_applicable_preprint HuggingFace revision 53a5bc98d49247bcf967500292575c3d3602de31; Figshare DOI 10.25452/figshare.plus.29190726 https://huggingface.co/datasets/Xaira-Therapeutics/X-Atlas-Orion/tree/53a5bc98d49247bcf967500292575c3d3602de31 Xaira Therapeutics X-Atlas Orion official release https://huggingface.co/datasets/Xaira-Therapeutics/X-Atlas-Orion/tree/53a5bc98d49247bcf967500292575c3d3602de31 CC BY-NC-SA 4.0 https://huggingface.co/datasets/Xaira-Therapeutics/X-Atlas-Orion/blob/53a5bc98d49247bcf967500292575c3d3602de31/LICENSE.md PERMITTED_ONLY_FOR_NONCOMMERCIAL_BY_NC_SA_COMPLIANT_RELEASE medium_high Publish as a separately licensed noncommercial component; attribute Xaira/X-Atlas, link the license, identify changes, and license the adaptation under CC BY-NC-SA 4.0 The source is the official fixed-revision Parquet release, not raw sequencing. NC and SA restrictions prevent presenting the mixed release as unrestricted or commercially reusable.
|
| 3 |
+
scPerturb AissaBenevolenskaya2021 10.1038/s41467-021-21884-z 33712615 GSE149383 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE149383 scPerturb v1.4 https://zenodo.org/records/13350497 CC BY 4.0 https://zenodo.org/records/13350497 PERMITTED_WITH_CC_BY_4_ATTRIBUTION_AND_CHANGE_NOTICE low Cite scPerturb and the original study; retain a CC BY 4.0 notice/link and state that CellClip normalized, subsetted, split, and otherwise modified the data The redistribution basis is the explicit license on the scPerturb v1.4 Zenodo dataset release, not merely public availability of the original GEO record.
|
| 4 |
+
scPerturb ChangYe2021 10.1038/s41587-021-01005-3 34531539 E-MTAB-10698; EGAS00001005405 https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-10698 scPerturb v1.4 https://zenodo.org/records/13350497 CC BY 4.0 https://zenodo.org/records/13350497 PERMITTED_WITH_CC_BY_4_ATTRIBUTION_AND_CHANGE_NOTICE low Cite scPerturb and the original study; retain a CC BY 4.0 notice/link and state that CellClip normalized, subsetted, split, and otherwise modified the data Nature's data-availability statement lists both E-MTAB-10698 and controlled-access EGA study EGAS00001005405; the redistribution basis for the packaged derivative is scPerturb v1.4 CC BY 4.0.
|
| 5 |
+
scPerturb LotfollahiTheis2023 10.15252/msb.202211517 37154091 GSE206741 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE206741 scPerturb v1.4 https://zenodo.org/records/13350497 CC BY 4.0 https://zenodo.org/records/13350497 PERMITTED_WITH_CC_BY_4_ATTRIBUTION_AND_CHANGE_NOTICE low Cite scPerturb and the original study; retain a CC BY 4.0 notice/link and state that CellClip normalized, subsetted, split, and otherwise modified the data The original paper is also CC BY 4.0, but the consistent release basis used here is the explicit scPerturb v1.4 dataset license.
|
| 6 |
+
scPerturb McFarlandTsherniak2020 10.1038/s41467-020-17440-w 32855387 Figshare DOI 10.6084/m9.figshare.5863776.v1 https://doi.org/10.6084/m9.figshare.5863776.v1 scPerturb v1.4 https://zenodo.org/records/13350497 CC BY 4.0 https://zenodo.org/records/13350497 PERMITTED_WITH_CC_BY_4_ATTRIBUTION_AND_CHANGE_NOTICE low Cite scPerturb and the original study; retain a CC BY 4.0 notice/link and state that CellClip normalized, subsetted, split, and otherwise modified the data The redistribution basis is the explicit license on the scPerturb v1.4 Zenodo dataset release.
|
| 7 |
+
scPerturb SrivatsanTrapnell2020 10.1126/science.aax6234 31806696 GSE139944 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE139944 scPerturb v1.4 https://zenodo.org/records/13350497 CC BY 4.0 https://zenodo.org/records/13350497 PERMITTED_WITH_CC_BY_4_ATTRIBUTION_AND_CHANGE_NOTICE low Cite scPerturb and the original study; retain a CC BY 4.0 notice/link and state that CellClip normalized, subsetted, split, and otherwise modified the data The redistribution basis is the explicit license on the scPerturb v1.4 Zenodo dataset release.
|
| 8 |
+
scPerturb ZhaoSims2021 10.1186/s13073-021-00894-y 33975634 GSE148842 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE148842 scPerturb v1.4 https://zenodo.org/records/13350497 CC BY 4.0 https://zenodo.org/records/13350497 PERMITTED_WITH_CC_BY_4_ATTRIBUTION_AND_CHANGE_NOTICE low Cite scPerturb and the original study; retain a CC BY 4.0 notice/link and state that CellClip normalized, subsetted, split, and otherwise modified the data The redistribution basis is the explicit license on the scPerturb v1.4 Zenodo dataset release.
|
| 9 |
+
scPerturb AdamsonWeissman2016 10.1016/j.cell.2016.11.048 27984733 GSE90546 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE90546 scPerturb v1.4 https://zenodo.org/records/13350497 CC BY 4.0 https://zenodo.org/records/13350497 PERMITTED_WITH_CC_BY_4_ATTRIBUTION_AND_CHANGE_NOTICE low Cite scPerturb and the original study; retain a CC BY 4.0 notice/link and state that CellClip normalized, subsetted, split, and otherwise modified the data The redistribution basis is the explicit license on the scPerturb v1.4 Zenodo dataset release.
|
| 10 |
+
scPerturb DatlingerBock2017 10.1038/nmeth.4177 28099430 GSE92872 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE92872 scPerturb v1.4 https://zenodo.org/records/13350497 CC BY 4.0 https://zenodo.org/records/13350497 PERMITTED_WITH_CC_BY_4_ATTRIBUTION_AND_CHANGE_NOTICE low Cite scPerturb and the original study; retain a CC BY 4.0 notice/link and state that CellClip normalized, subsetted, split, and otherwise modified the data The redistribution basis is the explicit license on the scPerturb v1.4 Zenodo dataset release.
|
| 11 |
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scPerturb DatlingerBock2021 10.1038/s41592-021-01153-z 34059827 GSE168620 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE168620 scPerturb v1.4 https://zenodo.org/records/13350497 CC BY 4.0 https://zenodo.org/records/13350497 PERMITTED_WITH_CC_BY_4_ATTRIBUTION_AND_CHANGE_NOTICE low Cite scPerturb and the original study; retain a CC BY 4.0 notice/link and state that CellClip normalized, subsetted, split, and otherwise modified the data The redistribution basis is the explicit license on the scPerturb v1.4 Zenodo dataset release.
|
| 12 |
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scPerturb DixitRegev2016 10.1016/j.cell.2016.11.038 27984732 GSE90063 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE90063 scPerturb v1.4 https://zenodo.org/records/13350497 CC BY 4.0 https://zenodo.org/records/13350497 PERMITTED_WITH_CC_BY_4_ATTRIBUTION_AND_CHANGE_NOTICE low Cite scPerturb and the original study; retain a CC BY 4.0 notice/link and state that CellClip normalized, subsetted, split, and otherwise modified the data The redistribution basis is the explicit license on the scPerturb v1.4 Zenodo dataset release.
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| 13 |
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scPerturb FrangiehIzar2021 10.1038/s41588-021-00779-1 33649592 SCP1064 https://singlecell.broadinstitute.org/single_cell/study/SCP1064/multi-modal-pooled-perturb-cite-seq-screens-in-patient-models-define-novel-mechanisms-of-cancer-immune-evasion scPerturb v1.4 https://zenodo.org/records/13350497 CC BY 4.0 https://zenodo.org/records/13350497 PERMITTED_WITH_CC_BY_4_ATTRIBUTION_AND_CHANGE_NOTICE low Cite scPerturb and the original study; retain a CC BY 4.0 notice/link and state that CellClip normalized, subsetted, split, and otherwise modified the data The redistribution basis is the explicit license on the scPerturb v1.4 Zenodo dataset release.
|
| 14 |
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scPerturb NadigOConner2024 10.1038/s41588-025-02169-3 40259084 GSE264667; PRJNA1100571 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE264667 scPerturb v1.4 https://zenodo.org/records/13350497 CC BY 4.0 https://zenodo.org/records/13350497 PERMITTED_WITH_CC_BY_4_ATTRIBUTION_AND_CHANGE_NOTICE low Cite scPerturb and the final peer-reviewed original study; retain a CC BY 4.0 notice/link and state that CellClip normalized, subsetted, split, and otherwise modified the data The manifest's 2024 label reflects preprint timing; use the 2025 final Nature Genetics citation and its GEO/SRA accessions. The cited Zenodo v1.4 record explicitly lists NadigOConner2024_hepg2.h5ad and NadigOConner2024_jurkat.h5ad under its CC BY 4.0 release.
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| 15 |
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scPerturb NormanWeissman2019 10.1126/science.aax4438 31395745 GSE133344 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE133344 scPerturb v1.4 https://zenodo.org/records/13350497 CC BY 4.0 https://zenodo.org/records/13350497 PERMITTED_WITH_CC_BY_4_ATTRIBUTION_AND_CHANGE_NOTICE low Cite scPerturb and the original study; retain a CC BY 4.0 notice/link and state that CellClip normalized, subsetted, split, and otherwise modified the data The redistribution basis is the explicit license on the scPerturb v1.4 Zenodo dataset release.
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| 16 |
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scPerturb PapalexiSatija2021 10.1038/s41588-021-00778-2 33649593 GSE153056 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE153056 scPerturb v1.4 https://zenodo.org/records/13350497 CC BY 4.0 https://zenodo.org/records/13350497 PERMITTED_WITH_CC_BY_4_ATTRIBUTION_AND_CHANGE_NOTICE low Cite scPerturb and the original study; retain a CC BY 4.0 notice/link and state that CellClip normalized, subsetted, split, and otherwise modified the data The redistribution basis is the explicit license on the scPerturb v1.4 Zenodo dataset release.
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| 17 |
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scPerturb ReplogleWeissman2022 10.1016/j.cell.2022.05.013 35688146 PRJNA831566; Figshare DOI 10.25452/figshare.plus.20022944 https://www.ncbi.nlm.nih.gov/bioproject/PRJNA831566 scPerturb v1.4 https://zenodo.org/records/13350497 CC BY 4.0 https://zenodo.org/records/13350497 PERMITTED_WITH_CC_BY_4_ATTRIBUTION_AND_CHANGE_NOTICE low Cite scPerturb and the original study; retain a CC BY 4.0 notice/link and state that CellClip normalized, subsetted, split, and otherwise modified the data Raw reads are in PRJNA831566; processed source data are also associated with https://doi.org/10.25452/figshare.plus.20022944 and gwps.wi.mit.edu.
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manifest/STUDY_SUMMARY.tsv
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source modality study_id n_training_units n_cells n_reference_cells n_effect_cells n_conditions n_targets cell_contexts contexts reference_definitions reference_selectors effect_selectors matrix_semantics counts_available feature_id_namespaces n_units_with_ensembl_fallback batch_info batch_metadata_status n_units_with_batch_metadata n_default_train_eligible_units n_target_filter_units n_engineered_construct_units source_collection audit_boundary remaining_risk collection_data_license license_evidence_url redistribution_status redistribution_risk perturbation_methods perturbation_direction_classes stage1_bridge_roles n_strict_stage1_method_eligible_units
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XCell genepert XAtlasOrion2025 2 7943468 384615 7558853 36604 36604 HCT116; HEK293T day7_post_transduction author field gene_target=Non-Targeting is_control=true (identical to is_reference) is_control=false normalize_total_10000_then_natural_log1p True gene_symbol_plus_ensembl_gene_id_fallback 2 available:109_author_sample_GEM_batches; available:223_author_sample_GEM_batches available 2 2 0 0 Xaira Therapeutics X-Atlas/Orion official Hugging Face release Official fixed-revision Parquet release converted and validated; raw shards not bundled CC BY-NC-SA 4.0 source license; author sample is a GEM batch, not a biological replicate CC BY-NC-SA 4.0 https://huggingface.co/datasets/Xaira-Therapeutics/X-Atlas-Orion/blob/53a5bc98d49247bcf967500292575c3d3602de31/LICENSE.md PERMITTED_ONLY_FOR_NONCOMMERCIAL_BY_NC_SA_COMPLIANT_RELEASE medium_high CRISPRi transcriptional_repression inhibitor 2
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| 3 |
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scPerturb chempert AissaBenevolenskaya2021 1 104491 28326 76165 3 3 PC9_xenograft subcutaneous_xenograft_in_vivo vehicle_only_no_measured_untreated_t0 is_reference=true; vehicle/DMSO is never untreated_t0 is_reference=false normalize_total_10000_then_natural_log1p True gene_symbol_only_as_released 0 available:4 available 1 1 0 0 scPerturb release v1.4; raw/source evidence not bundled Historical source evidence was reviewed before packaging but is not bundled no package-level exception recorded CC BY 4.0 https://zenodo.org/records/13350497 PERMITTED_WITH_CC_BY_4_ATTRIBUTION_AND_CHANGE_NOTICE low small_molecule chemical_perturbation not_applicable 0
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| 4 |
+
scPerturb chempert ChangYe2021 1 42277 21043 21234 3 3 PC9 standard_culture_trace_seq measured_untreated_t0_shared_by_three_96h_drug_conditions is_reference=true; vehicle/DMSO is never untreated_t0 is_reference=false normalize_total_10000_then_natural_log1p True gene_symbol_only_as_released 0 available:4 available 1 1 0 0 scPerturb release v1.4; raw/source evidence not bundled Historical source evidence was reviewed before packaging but is not bundled no package-level exception recorded CC BY 4.0 https://zenodo.org/records/13350497 PERMITTED_WITH_CC_BY_4_ATTRIBUTION_AND_CHANGE_NOTICE low small_molecule chemical_perturbation not_applicable 0
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| 5 |
+
scPerturb chempert LotfollahiTheis2023 2 75871 2902 72969 37 37 A549 standard_culture DMSO_DMSO_vehicle_only_no_measured_untreated_t0 is_reference=true; vehicle/DMSO is never untreated_t0 is_reference=false normalize_total_10000_then_natural_log1p True gene_symbol_only_as_released 0 available:21; available:96 available 2 2 0 0 scPerturb release v1.4; raw/source evidence not bundled Historical source evidence was reviewed before packaging but is not bundled no package-level exception recorded CC BY 4.0 https://zenodo.org/records/13350497 PERMITTED_WITH_CC_BY_4_ATTRIBUTION_AND_CHANGE_NOTICE low small_molecule chemical_perturbation not_applicable 0
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| 6 |
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scPerturb chempert McFarlandTsherniak2020 202 42209 10670 31539 776 776 253JBV; 5637; 639V; 786O; 8505C; A549; BICR31; BICR6; BT474; BT549; BXPC3; CAL29; CAOV3; CCFSTTG1; COLO680N; COLO829; CORL23; COV434; DKMG; FTC238; GAMG; GB1; GI1; HCC1143; HCC1806; HCT116; HCT15; HEC1A; HS294T; HT29; IALM; IGROV1; KP2; KU1919; KYSE510; LNCAPCLONEFGC; LOVO; LOXIMVI; LS1034; LU99; MCAS; MDAMB435S; MESSA; NCIH1339; NCIH1355; NCIH1437; NCIH1650; NCIH1793; NCIH1975; NCIH2009; NCIH226; NCIH2347; NCIH322; NCIN87; NIHOVCAR3; NMCG1; ONS76; OVISE; PATU8988T; RCC10RGB; RCM1; RERFLCAD1; RMUGS; S117; SH10TC; SKMEL2; SKMEL3; SKNFI; SKNSH; SNB75; SNU1079; SNU1105; SNU410; SNU761; SNU8; SNU840; SNUC2A; SQ1; SUIT2; TCCPAN2; TE8; TEN; UMUC1; WM1799 MIX_Seq__253JBV__expt10__24h; MIX_Seq__5637__expt10__24h; MIX_Seq__639V__expt10__24h; MIX_Seq__786O__expt10__24h; MIX_Seq__8505C__expt10__24h; MIX_Seq__A549__expt10__24h; MIX_Seq__BICR31__expt10__24h; MIX_Seq__BICR31__trametinib_timecourse; MIX_Seq__BICR6__expt10__24h; MIX_Seq__BICR6__trametinib_timecourse; MIX_Seq__BT474__trametinib_timecourse; MIX_Seq__BT549__expt10__24h; MIX_Seq__BT549__trametinib_timecourse; MIX_Seq__BXPC3__expt10__24h; MIX_Seq__CAL29__expt10__24h; MIX_Seq__CAOV3__expt10__24h; MIX_Seq__CAOV3__trametinib_timecourse; MIX_Seq__CCFSTTG1__expt10__24h; MIX_Seq__CCFSTTG1__trametinib_timecourse; MIX_Seq__COLO680N__expt10__24h; MIX_Seq__COLO680N__trametinib_timecourse; MIX_Seq__COLO829__expt10__24h; MIX_Seq__CORL23__expt10__24h; MIX_Seq__COV434__expt10__24h; MIX_Seq__COV434__trametinib_timecourse; MIX_Seq__DKMG__expt10__24h; MIX_Seq__DKMG__trametinib_timecourse; MIX_Seq__FTC238__expt10__24h; MIX_Seq__GAMG__expt10__24h; MIX_Seq__GB1__expt10__24h; MIX_Seq__GI1__expt10__24h; MIX_Seq__HCC1143__expt10__24h; MIX_Seq__HCC1806__expt10__24h; MIX_Seq__HCT116__expt10__24h; MIX_Seq__HCT15__expt10__24h; MIX_Seq__HEC1A__expt10__24h; MIX_Seq__HS294T__expt10__24h; MIX_Seq__HT29__expt10__24h; MIX_Seq__IALM__expt10__24h; MIX_Seq__IALM__trametinib_timecourse; MIX_Seq__IGROV1__expt10__24h; MIX_Seq__KP2__expt10__24h; MIX_Seq__KU1919__expt10__24h; MIX_Seq__KYSE510__expt10__24h; MIX_Seq__LNCAPCLONEFGC__expt10__24h; MIX_Seq__LNCAPCLONEFGC__trametinib_timecourse; MIX_Seq__LOVO__expt10__24h; MIX_Seq__LOXIMVI__expt10__24h; MIX_Seq__LS1034__expt10__24h; MIX_Seq__LS1034__trametinib_timecourse; MIX_Seq__LU99__expt10__24h; MIX_Seq__MCAS__expt10__24h; MIX_Seq__MDAMB435S__expt10__24h; MIX_Seq__MESSA__expt10__24h; MIX_Seq__NCIH1339__expt10__24h; MIX_Seq__NCIH1355__expt10__24h; MIX_Seq__NCIH1437__expt10__24h; MIX_Seq__NCIH1650__expt10__24h; MIX_Seq__NCIH1793__expt10__24h; MIX_Seq__NCIH1975__expt10__24h; MIX_Seq__NCIH2009__expt10__24h; MIX_Seq__NCIH226__expt10__24h; MIX_Seq__NCIH226__trametinib_timecourse; MIX_Seq__NCIH2347__expt10__24h; MIX_Seq__NCIH2347__trametinib_timecourse; MIX_Seq__NCIH322__expt10__24h; MIX_Seq__NCIN87__expt10__24h; MIX_Seq__NIHOVCAR3__expt10__24h; MIX_Seq__NMCG1__expt10__24h; MIX_Seq__ONS76__expt10__24h; MIX_Seq__OVISE__expt10__24h; MIX_Seq__PATU8988T__expt10__24h; MIX_Seq__RCC10RGB__expt10__24h; MIX_Seq__RCC10RGB__trametinib_timecourse; MIX_Seq__RCM1__expt10__24h; MIX_Seq__RCM1__trametinib_timecourse; MIX_Seq__RERFLCAD1__expt10__24h; MIX_Seq__RERFLCAD1__trametinib_timecourse; MIX_Seq__RMUGS__expt10__24h; MIX_Seq__S117__expt10__24h; MIX_Seq__SH10TC__expt10__24h; MIX_Seq__SH10TC__trametinib_timecourse; MIX_Seq__SKMEL2__trametinib_timecourse; MIX_Seq__SKMEL3__expt10__24h; MIX_Seq__SKMEL3__trametinib_timecourse; MIX_Seq__SKNFI__expt10__24h; MIX_Seq__SKNSH__expt10__24h; MIX_Seq__SNB75__expt10__24h; MIX_Seq__SNU1079__expt10__24h; MIX_Seq__SNU1079__trametinib_timecourse; MIX_Seq__SNU1105__expt10__24h; MIX_Seq__SNU410__expt10__24h; MIX_Seq__SNU761__expt10__24h; MIX_Seq__SNU840__expt10__24h; MIX_Seq__SNU8__expt10__24h; MIX_Seq__SNUC2A__expt10__24h; MIX_Seq__SQ1__expt10__24h; MIX_Seq__SQ1__trametinib_timecourse; MIX_Seq__SUIT2__expt10__24h; MIX_Seq__TCCPAN2__expt10__24h; MIX_Seq__TE8__expt10__24h; MIX_Seq__TEN__expt10__24h; MIX_Seq__TEN__trametinib_timecourse; MIX_Seq__UMUC1__expt10__24h; MIX_Seq__UMUC1__trametinib_timecourse; MIX_Seq__WM1799__expt10__24h same_cell_line__expt10__24h__explicit_DMSO_vehicle_across_author_treatment_channels; no_measured_untreated_t0; same_cell_line_time_channel__explicit_hash_tag_DMSO_vehicle; Untreated_48hr_is_excluded_not_t0 is_reference=true; vehicle/DMSO is never untreated_t0 is_reference=false normalize_total_10000_then_natural_log1p True gene_symbol_only_as_released 0 available:2; available:9 available 202 202 0 0 scPerturb release v1.4; raw/source evidence not bundled Historical source evidence was reviewed before packaging but is not bundled no package-level exception recorded CC BY 4.0 https://zenodo.org/records/13350497 PERMITTED_WITH_CC_BY_4_ATTRIBUTION_AND_CHANGE_NOTICE low small_molecule chemical_perturbation not_applicable 0
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| 7 |
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scPerturb chempert SrivatsanTrapnell2020 14 885777 38223 847554 2664 2664 A549; K562; MCF7 sci_Plex2__A549__BMS-345541__dose_response; sci_Plex2__A549__dexamethasone__dose_response; sci_Plex2__A549__nutlin-3a__dose_response; sci_Plex2__A549__vorinostat_SAHA__dose_response; sci_Plex3__A549__24h; sci_Plex3__A549__72h; sci_Plex3__K562__24h; sci_Plex3__MCF7__24h; sci_Plex4__A549__24h__combination; sci_Plex4__A549__24h__hdaci_single; sci_Plex4__A549__24h__metabolic_single; sci_Plex4__MCF7__24h__combination; sci_Plex4__MCF7__24h__hdaci_single; sci_Plex4__MCF7__24h__metabolic_single cell_line_24h_vehicle; strict_DMSO_DMSO_global_vehicle is distinguished from named_zero_active_dose_matched_vehicle_series; plate is preserved as batch but does not universally carry its own DMSO control; same_cell_line_time_replicate_plate__control_0nM_vehicle; same_drug__author_hash_sheet_repeat__zero_dose_vehicle; solvent_identity_not_recovered_so vehicle is never called untreated_t0 is_reference=true; vehicle/DMSO is never untreated_t0 is_reference=false normalize_total_10000_then_natural_log1p True gene_symbol_only_as_released 0 available:16; available:2; available:3; available:4 available 14 14 0 0 scPerturb release v1.4; raw/source evidence not bundled Historical source evidence was reviewed before packaging but is not bundled no package-level exception recorded CC BY 4.0 https://zenodo.org/records/13350497 PERMITTED_WITH_CC_BY_4_ATTRIBUTION_AND_CHANGE_NOTICE low small_molecule chemical_perturbation not_applicable 0
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| 8 |
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scPerturb chempert ZhaoSims2021 9 155377 77942 77435 17 17 GBM_PW029; GBM_PW030; GBM_PW032; GBM_PW034; GBM_PW036; GBM_PW040; GBM_PW051; GBM_PW052; GBM_PW053 acute_slice_culture__PW029__18h; acute_slice_culture__PW030__18h; acute_slice_culture__PW032__18h; acute_slice_culture__PW034__18h; acute_slice_culture__PW036__18h; acute_slice_culture__PW040__18h; acute_slice_culture__PW051__18h; acute_slice_culture__PW052__18h; acute_slice_culture__PW053__18h same_patient__acute_slice__18h__GEO_annotated_DMSO_vehicle; native_biopsy_is_excluded_not_t0 is_reference=true; vehicle/DMSO is never untreated_t0 is_reference=false normalize_total_10000_then_natural_log1p True gene_symbol_only_as_released 0 available:2; available:3; available:4; available:5; available:7; available:8 available 9 9 0 0 scPerturb release v1.4; raw/source evidence not bundled Historical source evidence was reviewed before packaging but is not bundled no package-level exception recorded CC BY 4.0 https://zenodo.org/records/13350497 PERMITTED_WITH_CC_BY_4_ATTRIBUTION_AND_CHANGE_NOTICE low small_molecule chemical_perturbation not_applicable 0
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| 9 |
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scPerturb genepert AdamsonWeissman2016 5 65091 5542 59549 110 98 K562 dmso_vehicle; standard_culture; thapsigargin_100nm; tunicamycin_4ug_per_ml author-verified NTC/scramble/safe-target/exogenous reference is_control=true (identical to is_reference) is_control=false; for vocabulary training apply target_gene_symbol_status=mapped_to_foundation_vocab normalize_total_10000_then_natural_log1p True gene_symbol_only_as_released 0 available:1; available:10; unavailable_or_not_reported available; unavailable_or_not_reported 4 5 0 0 scPerturb release v1.4; raw/source evidence not bundled Historical source evidence was reviewed before packaging but is not bundled some units lack batch metadata CC BY 4.0 https://zenodo.org/records/13350497 PERMITTED_WITH_CC_BY_4_ATTRIBUTION_AND_CHANGE_NOTICE low CRISPRi;CRISPRi_three_guide_vector transcriptional_repression inhibitor 5
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| 10 |
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scPerturb genepert DatlingerBock2017 2 5905 1320 4585 64 64 Jurkat stimulated; unstimulated author-verified NTC/scramble/safe-target/exogenous reference is_control=true (identical to is_reference) is_control=false; for vocabulary training apply target_gene_symbol_status=mapped_to_foundation_vocab normalize_total_10000_then_natural_log1p True gene_symbol_only_as_released 0 available:5; available:6 available 2 2 0 0 scPerturb release v1.4; raw/source evidence not bundled Historical source evidence was reviewed before packaging but is not bundled no package-level exception recorded CC BY 4.0 https://zenodo.org/records/13350497 PERMITTED_WITH_CC_BY_4_ATTRIBUTION_AND_CHANGE_NOTICE low CRISPRko gene_loss_of_function inhibitor 2
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| 11 |
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scPerturb genepert DatlingerBock2021 2 39194 4497 34697 80 80 Jurkat stimulated; unstimulated author-verified NTC/scramble/safe-target/exogenous reference is_control=true (identical to is_reference) is_control=false; for vocabulary training apply target_gene_symbol_status=mapped_to_foundation_vocab normalize_total_10000_then_natural_log1p True gene_symbol_plus_ensembl_gene_id_fallback 2 available:192 available 2 2 0 0 scPerturb release v1.4; raw/source evidence not bundled Historical source evidence was reviewed before packaging but is not bundled no package-level exception recorded CC BY 4.0 https://zenodo.org/records/13350497 PERMITTED_WITH_CC_BY_4_ATTRIBUTION_AND_CHANGE_NOTICE low CRISPRko gene_loss_of_function inhibitor 2
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| 12 |
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scPerturb genepert DixitRegev2016 2 43883 8872 35011 20 20 K562 standard_culture author-verified NTC/scramble/safe-target/exogenous reference is_control=true (identical to is_reference) is_control=false; for vocabulary training apply target_gene_symbol_status=mapped_to_foundation_vocab normalize_total_10000_then_natural_log1p True gene_symbol_only_as_released 0 unavailable_or_not_reported unavailable_or_not_reported 0 2 0 0 scPerturb release v1.4; raw/source evidence not bundled Historical source evidence was reviewed before packaging but is not bundled some units lack batch metadata CC BY 4.0 https://zenodo.org/records/13350497 PERMITTED_WITH_CC_BY_4_ATTRIBUTION_AND_CHANGE_NOTICE low CRISPRko gene_loss_of_function inhibitor 2
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| 13 |
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scPerturb genepert FrangiehIzar2021 3 218331 57605 160726 744 744 melanoma_cell_line ifng; ifng_then_til_coculture; untreated author-verified NTC/scramble/safe-target/exogenous reference is_control=true (identical to is_reference) is_control=false; for vocabulary training apply target_gene_symbol_status=mapped_to_foundation_vocab normalize_total_10000_then_natural_log1p True gene_symbol_only_as_released 0 unavailable_or_not_reported unavailable_or_not_reported 0 3 0 0 scPerturb release v1.4; raw/source evidence not bundled Historical source evidence was reviewed before packaging but is not bundled some units lack batch metadata CC BY 4.0 https://zenodo.org/records/13350497 PERMITTED_WITH_CC_BY_4_ATTRIBUTION_AND_CHANGE_NOTICE low CRISPRko gene_loss_of_function inhibitor 3
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| 14 |
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scPerturb genepert NadigOConner2024 2 408429 16989 391440 4786 4786 HepG2; Jurkat standard_culture author-verified NTC/scramble/safe-target/exogenous reference is_control=true (identical to is_reference) is_control=false; for vocabulary training apply target_gene_symbol_status=mapped_to_foundation_vocab normalize_total_10000_then_natural_log1p True gene_symbol_only_as_released 0 available:55; available:56 available 2 2 2 0 scPerturb release v1.4; raw/source evidence not bundled Historical source evidence was reviewed before packaging but is not bundled 2 unit(s) require target filtering CC BY 4.0 https://zenodo.org/records/13350497 PERMITTED_WITH_CC_BY_4_ATTRIBUTION_AND_CHANGE_NOTICE low CRISPRi transcriptional_repression inhibitor 2
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| 15 |
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scPerturb genepert NormanWeissman2019 2 115690 22366 93324 236 178 K562 standard_culture author-verified NTC/scramble/safe-target/exogenous reference is_control=true (identical to is_reference) is_control=false; for vocabulary training apply target_gene_symbol_status=mapped_to_foundation_vocab normalize_total_10000_then_natural_log1p True gene_symbol_only_as_released 0 available:8 available 2 1 0 0 scPerturb release v1.4; raw/source evidence not bundled Historical source evidence was reviewed before packaging but is not bundled no package-level exception recorded CC BY 4.0 https://zenodo.org/records/13350497 PERMITTED_WITH_CC_BY_4_ATTRIBUTION_AND_CHANGE_NOTICE low CRISPRa transcriptional_activation activator 2
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| 16 |
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scPerturb genepert PapalexiSatija2021 2 24400 3727 20673 35 35 THP1 arrayed_validation; dac_tgfb1_ifng_stimulated author-verified NTC/scramble/safe-target/exogenous reference is_control=true (identical to is_reference) is_control=false; for vocabulary training apply target_gene_symbol_status=mapped_to_foundation_vocab normalize_total_10000_then_natural_log1p True gene_symbol_only_as_released 0 available:15; available:3 available 2 2 0 0 scPerturb release v1.4; raw/source evidence not bundled Historical source evidence was reviewed before packaging but is not bundled no package-level exception recorded CC BY 4.0 https://zenodo.org/records/13350497 PERMITTED_WITH_CC_BY_4_ATTRIBUTION_AND_CHANGE_NOTICE low CRISPRko gene_loss_of_function inhibitor 2
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| 17 |
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scPerturb genepert ReplogleWeissman2022 3 2547877 97504 2450373 14316 14316 K562; RPE1 standard_culture author-verified NTC/scramble/safe-target/exogenous reference is_control=true (identical to is_reference) is_control=false; for vocabulary training apply target_gene_symbol_status=mapped_to_foundation_vocab normalize_total_10000_then_natural_log1p True gene_symbol_only_as_released 0 available:267; available:48; available:56 available 3 3 3 0 scPerturb release v1.4; raw/source evidence not bundled Historical source evidence was reviewed before packaging but is not bundled 3 unit(s) require target filtering CC BY 4.0 https://zenodo.org/records/13350497 PERMITTED_WITH_CC_BY_4_ATTRIBUTION_AND_CHANGE_NOTICE low CRISPRi transcriptional_repression inhibitor 3
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manifest/TRAINING_UNITS.tsv
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manifest/UPLOAD_MANIFEST.tsv
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