benchmark_id,pmid,paper_doi,paper_title,year,journal,dataset_accession,secondary_accession,species,cell_type_original,cell_type_standard,cell_type_markers,tissue,source_type,cell_context,disease,platform,perturbation_type,perturbation_scope,perturbation_name,smiles,description,control_type,dose_design,time_design
32094658_01,32094658,10.1038/s41587-020-0430-6,Targeting the cytoskeleton to direct pancreatic differentiation of human pluripotent stem cells,2020,Nature biotechnology,GSE137659,PRJNA566163,human,,,,Pancreas,cell_line,human pancreatic progenitors from HUES8 hESC line,none,10x Chromium,drug,single,latrunculin A,CC1CCC2CC(CC(O2)(C3CSC(=O)N3)O)OC(=O)C=C(CCC=CC=C1)C,Pancreatic progenitors from HUES8 hESC line treated with latrunculin A.,untreated,single,multi
33712615_01,33712615,10.1038/s41467-021-21884-z,Single-cell transcriptional changes associated with drug tolerance and response to combination therapies in cancer,2021,Nature communications,GSE149383,,human,PC9,PC9,,Lung,cell_line,human NSCLC cell line,non-small cell lung cancer,"Drop-seq, 10x Genomics Chromium",drug,single,erlotinib,COCCOC1=C(C=C2C(=C1)C(=NC=N2)NC3=CC=CC(=C3)C#C)OCCOC,PC9 NSCLC cell line treated with erlotinib EGFR TKI.,untreated,single,multi
32846134_01,32846134,10.1016/j.celrep.2020.108077,Single-Cell Transcriptome Analysis of Colon Cancer Cell Response to 5-Fluorouracil-Induced DNA Damage,2020,Cell reports,GSE149224,,human,RKO,RKO,,Colon,cell_line,RKO colon cancer cell line,colon cancer,Drop-seq,drug,single,5-fluorouracil,C1=C(C(=O)NC(=O)N1)F,RKO colon cancer cell line treated with 5-fluorouracil.,untreated,multi,single
38652658_01,38652658,10.1016/j.celrep.2024.114139,Multiplexed single-cell lineage tracing of mitotic kinesin inhibitor resistance in glioblastoma,2024,Cell reports,GSE239651,,human,,,,Brain,cell_line,human glioblastoma cell line,glioblastoma,Microwell-based scRNA-seq (Illumina NovaSeq 6000),drug,single,ispinesib,CC1=CC=C(C=C1)C(=O)N(CCCN)C(C2=NC3=C(C=CC(=C3)Cl)C(=O)N2CC4=CC=CC=C4)C(C)C,"TS543 glioblastoma neurospheres treated with ispinesib, a KIF11 inhibitor, profiled by scRNA-seq over a long-term time course with lineage tracing.",DMSO,single,multi
38895265_01,38895265,10.1101/2024.06.04.596911,TNBC response to paclitaxel phenocopies interferon response which reveals cell cycle-associated resistance mechanisms,2024,bioRxiv : the preprint server for biology,GSE266934,,human,,,,Breast,cell_line,human TNBC cell line,triple negative breast cancer,10x Chromium,drug,single,Paclitaxel,CC1=C2C(C(=O)C3(C(CC4C(C3C(C(C2(C)C)(CC1OC(=O)C(C(C5=CC=CC=C5)NC(=O)C6=CC=CC=C6)O)O)OC(=O)C7=CC=CC=C7)(CO4)OC(=O)C)O)C)OC(=O)C,HCC1143 TNBC cells treated with paclitaxel.,vehicle (DMSO),single,multi
38937474_01,38937474,10.1038/s41467-024-49360-4,Farnesyltransferase inhibition overcomes oncogene-addicted non-small cell lung cancer adaptive resistance to targeted therapies,2024,Nature communications,GSE248450,,human,,,,Lung,cell_line,human EGFR-mutant NSCLC cell line,non-small cell lung cancer,10x Chromium,drug,single,osimertinib,CN1C=C(C2=CC=CC=C21)C3=NC(=NC=C3)NC4=C(C=C(C(=C4)NC(=O)C=C)N(C)CCN(C)C)OC,HCC4006 EGFR-mutant NSCLC cell line treated with osimertinib.,untreated,single,single
39803533_01,39803533,10.1101/2024.12.26.630414,Quantitative analyses of single mitochondrial structure-function heterogeneity uncovers stemness specification by redox-tuned small-mitochondrial-networks,2025,bioRxiv,GSE285728,,human,,,,Skin,cell_line,human keratinocyte cell line,normal,10x Chromium,drug,single,TCDD,C1=C2C(=CC(=C1Cl)Cl)OC3=CC(=C(C=C3O2)Cl)Cl,HaCaT keratinocytes treated with TCDD.,vehicle,single,single
40166195_01,40166195,10.1101/2025.03.18.643980,Lineage Tracing Reveals Clone-Specific Responses to Doxorubicin in Triple-Negative Breast Cancer,2025,bioRxiv : the preprint server for biology,GSE291678,,human,,,,Breast,cell_line,human triple-negative breast cancer cell line,triple-negative breast cancer,10x Chromium,drug,single,doxorubicin,CC1C(C(CC(O1)OC2CC(CC3=C2C(=C4C(=C3O)C(=O)C5=C(C4=O)C(=CC=C5)OC)O)(C(=O)CO)O)N)O,MDA-MB-231 triple-negative breast cancer cells treated with doxorubicin and profiled by scRNA-seq after recovery.,untreated,single,multi
40766395_01,40766395,10.1101/2025.06.10.657506,Decoding Cellular Stress States for Toxicology Using Single-Cell Transcriptomics,2025,bioRxiv : the preprint server for biology,GSE299113,,human,,,,Liver,cell_line,human hepatic HepaRG cell line,liver toxicology model,TempO-LINC,drug,single,Brefeldin A,CC1CCCC=CC2CC(CC2C(C=CC(=O)O1)O)O,HepaRG cells treated with Brefeldin A.,DMSO,single,single
34591417_01,34591417,10.20892/j.issn.2095-3941.2021.0267,Single-cell trajectories of melanoma cell resistance to targeted treatment,2021,Cancer biology & medicine,GSE164897,PRJNA692421,human,,,,Skin,cell_line,human BRAF-mutant melanoma A375 cell line,melanoma,10x Chromium,drug,single,vemurafenib,CCCS(=O)(=O)NC1=C(C(=C(C=C1)F)C(=O)C2=CNC3=C2C=C(C=N3)C4=CC=C(C=C4)Cl)F,A375 BRAF-mutant melanoma cells treated with vemurafenib versus untreated.,untreated,single,single
34857732_01,34857732,10.1038/s41467-021-26840-5,Dynamic prostate cancer transcriptome analysis delineates the trajectory to disease progression,2021,Nature communications,E-MTAB-9903,,human,,,,Prostate,cell_line,human prostate cancer cell line,prostate cancer,10x Chromium,drug,single,GSK126,CCC(C)N1C=C(C2=C(C=C(C=C21)C3=CN=C(C=C3)N4CCNCC4)C(=O)NCC5=C(C=C(NC5=O)C)C)C,LNCaP prostate cancer cells treated with EZH2 inhibitor GSK126.,untreated,single,multi
35410383_01,35410383,10.1038/s41588-022-01047-6,H3K27me3 conditions chemotolerance in triple-negative breast cancer,2022,Nature genetics,GSE164715,PRJNA691624,human,,,,Breast,cell_line,human triple-negative breast cancer cell line,triple-negative breast cancer,10x Chromium 3' v3,drug,single,Fluorouracil,C1=C(C(=O)NC(=O)N1)F,MDA-MB-468 triple-negative breast cancer cells treated with Fluorouracil.,untreated,single,multi
41871169_01,41871169,10.1371/journal.ppat.1013610,Single-cell profiling of HDAC inhibitor-induced EBV lytic heterogeneity defines abortive and refractory states in B lymphoblasts,2026,PLoS pathogens,GSE319577,PRJNA1423778,human,,,,B lymphoblast,cell_line,human Burkitt lymphoma cell line,Burkitt lymphoma,10x Chromium,drug,single,panobinostat,CC1=C(C2=CC=CC=C2N1)CCNCC3=CC=C(C=C3)C=CC(=O)NO,P3HR1-ZHT Burkitt lymphoma cells treated with panobinostat.,untreated,single,single
37086265_01,37086265,10.18632/aging.204666,Single-cell transcriptomic analysis uncovers diverse and dynamic senescent cell populations,2023,Aging,GSE226225,PRJNA939187,human,,,,Lung,cell_line,human fetal lung fibroblast cell line,normal,10x Chromium,drug,single,etoposide,CC1OCC2C(O1)C(C(C(O2)OC3C4COC(=O)C4C(C5=CC6=C(C=C35)OCO6)C7=CC(=C(C(=C7)OC)O)OC)O)O,WI-38 fetal lung fibroblasts treated with etoposide over a 10-day time course.,untreated,single,multi
37732484_01,37732484,10.1161/ATVBAHA.123.319283,Single-Cell RNA Sequencing Reveals That Adaptation of Human Aortic Endothelial Cells to Antiproliferative Therapies Is Modulated by Flow-Induced Shear Stress,2023,"Arteriosclerosis, thrombosis, and vascular biology",GSE212388,PRJNA875289,human,,,,Aorta,cell_line,human aortic endothelial cells,healthy,Seq-Well,drug,single,paclitaxel,CC1=C2C(C(=O)C3(C(CC4C(C3C(C(C2(C)C)(CC1OC(=O)C(C(C5=CC=CC=C5)NC(=O)C6=CC=CC=C6)O)O)OC(=O)C7=CC=CC=C7)(CO4)OC(=O)C)O)C)OC(=O)C,Human aortic endothelial cells treated with paclitaxel.,untreated,single,single
36553506_01,36553506,10.3390/genes13122240,Single-Cell Sequencing Identifies Master Regulators Affected by Panobinostat in Neuroblastoma Cells,2022,Genes,GitHub: federicogiorgi/panobinostat,,human,,,,Brain,cell_line,human neuroblastoma cell line,neuroblastoma,10x Chromium,drug,single,panobinostat,CC1=C(C2=CC=CC=C2N1)CCNCC3=CC=C(C=C3)C=CC(=O)NO,Kelly neuroblastoma cells treated with panobinostat.,DMSO,single,single
38272949_02,38272949,10.1038/s41598-024-52311-0,Transcriptional characterization of iPSC-derived microglia as a model for therapeutic development in neurodegeneration,2024,Scientific reports,GSE226077,PRJNA938479,human,,,,Brain,cell_line,human iPSC-derived microglia,neurodegeneration,10x Chromium v3.1,drug,single,GW3965,C1=CC=C(C=C1)C(CN(CCCOC2=CC=CC(=C2)CC(=O)O)CC3=C(C(=CC=C3)C(F)(F)F)Cl)C4=CC=CC=C4,iPSC-derived microglia treated with GW3965.,DMSO,single,single
38589664_01,38589664,10.1038/s41698-024-00561-6,Mutational signature-based identification of DNA repair deficient gastroesophageal adenocarcinomas for therapeutic targeting,2024,NPJ precision oncology,GSE256301,PRJNA1078903,human,,,,Stomach,cell_line,human gastric adenocarcinoma cell line,gastric adenocarcinoma,10x Chromium,drug,single,cisplatin,N.N.Cl[Pt]Cl,NER-deficient NUGC3 gastric adenocarcinoma cells treated with cisplatin.,vehicle,single,single
36318267_01,36318267,10.1093/nar/gkac908,Estrogen regulates divergent transcriptional and epigenetic cell states in breast cancer,2022,Nucleic acids research,GSE154873,PRJNA647723,human,,,,Breast,cell_line,human ER+ breast cancer cell line,breast cancer,10x Chromium,drug,single,estradiol,CC12CCC3C(C1CCC2O)CCC4=C3C=CC(=C4)O,MCF-7 ER+ breast cancer cell line treated with estradiol.,untreated,single,multi
36382181_01,36382181,10.1016/j.csbj.2022.10.031,Reprogramming landscape highlighted by dynamic transcriptomes in therapy-induced neuroendocrine differentiation,2022,Computational and structural biotechnology journal,GSE215943,PRJNA891317,human,,,,Prostate,cell_line,human prostate cancer cell line,prostate cancer,10x Chromium,drug,single,enzalutamide,CC1(C(=O)N(C(=S)N1C2=CC(=C(C=C2)C(=O)NC)F)C3=CC(=C(C=C3)C#N)C(F)(F)F)C,"LNCaP prostate cancer cells treated with 5 uM enzalutamide over 4, 7, and 14 days.",DMSO,single,multi