data_table.csv

,Shorthand,Title,.h5ad availability,Treatment,# perturbations,# cell types,# doses,# timepoints,Reported cells total,Organism,Tissue,Technique,Data location,Panel size,Measurement,Cell source,Disease,Contrasts,Developmental stage,Number of reported cell types or clusters,Cell clustering,Pseudotime,RNA Velocity,PCA,tSNE,H5AD location,Isolation,BC --> Cell ID _OR_ BC --> Cluster ID,Number individuals
0,[Jaitin *et al.* Science](https://doi.org/10.1126/science.1247651),Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types,,CRISPR,8-22,1,-,1,"4,468",Mouse,Spleen,MARS-seq,GSE54006,,RNA-seq,CD11c+ enriched splenocytes,,,,9.0,Yes,No,,No,No,,Sorting (FACS),,
2,[Dixit *et al.* Cell](https://doi.org/10.1016/j.cell.2016.11.038),Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens, [\[raw h5ad\]](https://ndownloader.figshare.com/files/34011689) [\[processed h5ad\]](https://ndownloader.figshare.com/files/34014608) [\[processing nb\]](https://nbviewer.ipython.org/github/theislab/sc-pert/blob/main/datasets/Dixit_2016.ipynb),CRISPR,"10,24",1,-,1-2,"200,000","Human, Mouse",Culture,Perturb-seq,GSE90063,,RNA-seq,"BMDCs, K562",,,,,,,,,No,,Nanodroplet dilution,,
3,[Datlinger *et al.* NMeth](https://doi.org/10.1038/nmeth.4177),Pooled CRISPR screening with single-cell transcriptome readout,,CRISPR,29,1,-,1,"5,905","Human, Mouse",Culture,CROP-seq,GSE92872,,RNA-seq,"HEK293T, 3T3, Jurkat",,,,,,,,,No,,,,
4,[Hill *et al.* NMethods](https://doi.org/10.1038/nmeth.4604),On the design of CRISPR-based single-cell molecular screens,,CRISPR,32,1,2,1,"5,879",Human,Culture,CROP-seq,GSE108699,,RNA-seq,MCF10a cells,,,,,,,,,,,,https://github.com/shendurelab/single-cell-ko-screens#result-files,
13,[Ursu *et al.* bioRxiv](https://doi.org/10.1101/2020.11.16.383307),Massively parallel phenotyping of variant impact in cancer with Perturb-seq reveals a shift in the spectrum of cell states induced by somatic mutations,,CRISPR,200,1,-,1,"162,314",Human,Lung,Perturb-seq,,,RNA-seq,,,,,,,,,,,,,,
14,[Jin *et al.* Science](https://doi.org/10.1126/science.aaz6063),In vivo Perturb-Seq reveals neuronal and glial abnormalities associated with autism risk genes,,CRISPR,35,-,-,1,"46,770",Mouse,Brain,Perturb-seq,,,RNA-seq,,,,,,,,,,,,,,
15,[Frangieh *et al.* NGenetics](https://doi.org/10.1038/s41588-021-00779-1),Multimodal pooled Perturb-CITE-seq screens in patient models define mechanisms of cancer immune evasion, [\[raw h5ad\]](https://ndownloader.figshare.com/files/34012565) [\[processed h5ad\]](https://ndownloader.figshare.com/files/34013717) [\[processing nb\]](https://nbviewer.ipython.org/github/theislab/sc-pert/blob/main/datasets/Frangieh_2021.ipynb),CRISPR,248,1,-,1,"218,331",Human,Culture,Perturb-CITE-seq,SCP1064,,RNA-seq,,,,,,,,,,,,,,
16,[Papalexi *et al.* NGenetics](https://doi.org/10.1038/s41588-021-00778-2),Characterizing the molecular regulation of inhibitory immune checkpoints with multimodal single-cell screens,,CRISPR,111 (sgRNA),1,2,-,"28,295",Human,Culture,CITE-seq & ECCITE-seq,GSE153056,,RNA-seq,,,,,,,,,,,,,,
17,[Datlinger *et al.* NMethods](https://doi.org/10.1038/s41592-021-01153-z),Ultra-high-throughput single-cell RNA sequencing and perturbation screening with combinatorial fluidic indexing,,CRISPR KO + antibody,96,1,1,1,,"Human, Mouse",,scifi-RNA-seq,,,,,,,,,,,,,,,,,
11,[Alda-Catalinas *et al.* CSystems](https://doi.org/10.1016/j.cels.2020.06.004),A Single-Cell Transcriptomics CRISPR-Activation Screen Identifies Epigenetic Regulators of the Zygotic Genome Activation Program,,CRISPRa,230,1,-,-,"203,894",Mouse,Culture,Chromium,,,RNA-seq,mESCs,,,,,,,,,,,,,
19,[Norman *et al.* (2019)](https://doi.org/10.1126/science.aax4438),, [\[raw h5ad\]](https://ndownloader.figshare.com/files/34002548) [\[processed h5ad\]](https://ndownloader.figshare.com/files/34027562) [\[curation nb\]](https://nbviewer.ipython.org/github/theislab/sc-pert/blob/main/datasets/Norman_2019_curation.ipynb) [\[processing nb\]](https://nbviewer.ipython.org/github/theislab/sc-pert/blob/main/datasets/Norman_2019.ipynb),CRISPRa,287,1,-,1,,,,Perturb-seq,,,RNA-seq,induction of gene pair targets+single gene controls in K562 cells after screening 112 genes (2x gRNA per) and their combinations,,,,,,,,,,,,,
1,[Adamson *et al.* Cell](https://doi.org/10.1016/j.cell.2016.11.048),A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response,,CRISPRi,9-93 (sgRNA),1,-,1,"86,000",Human,Culture,Perturb-seq,GSE90546,,RNA-seq,K562,,,,,,,,,Yes,,,,
5,[Gasperini *et al.* Cell](https://doi.org/10.1016/j.cell.2018.11.029),A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens,,CRISPRi,"1119, 5779",1,-,1,"207,324",Human,Culture,CROP-seq,GSE120861,,RNA-seq,K562 Cells,,CRISPR Screen,,,,,,,,,,,
8,[Jost *et al.* NBT](https://doi.org/10.1038/s41587-019-0387-5),Titrating gene expression using libraries of systematically attenuated CRISPR guide RNAs,,CRISPRi,25,2,-,1,"19,587",Human,Culture,Perturb-seq,GSE132080,,RNA-seq,K562 cells,,25 gene screen,,,,,,,,,,,
10,[Schraivogel *et al.* NMethods](https://doi.org/10.1038/s41592-020-0837-5),Targeted Perturb-seq enables genome-scale genetic screens in single cells, [\[processing nb\]](https://nbviewer.ipython.org/github/theislab/sc-pert/blob/main/datasets/Schraivogel_2020.ipynb),CRISPRi,1778 (enhancers),1,-,1,"231,667","Human, Mouse","Bone marrow, Culture",TAP-seq,GSE135497,"1,000",RNA-seq,,,,,,,,,,Yes,,,,
18,[Leng *et al.* bioRxiv](https://doi.org/10.1101/2021.08.23.457400),CRISPRi screens in human astrocytes elucidate regulators of distinct inflammatory reactive states,,CRISPRi,30,1,2,-,,,,,,,,,,,,,,,,,,,,,
20,[Replogle *et al.* (2020)](https://doi.org/nan),,,genetic targets,,,,,,,,,,,,,,,,,,,,,,,,,
21,[Replogle *et al.* (2021)](https://doi.org/10.1101/2021.12.16.473013v3),,,genetic targets,>10000,2,-,-,,,,Perturb-seq,,,RNA-seq,,,,,,,,,,,,,,
6,[Shin *et al.* SAdvances](https://doi.org/10.1126/sciadv.aav2249),Multiplexed single-cell RNA-seq via transient barcoding for simultaneous expression profiling of various drug perturbations,,small molecules,45,2,1,1,"3,091","Mouse, Human",Culture,Drop-seq,PRJNA493658,,RNA-seq,"HEK293T, NIIH3T3, A375, SW480, K562",,45 perturbations,,,,,,,,,,,
7,[Srivatsan *et al.* Science](https://doi.org/10.1126/science.aax6234),Massively multiplex chemical transcriptomics at single-cell resolution, [\[raw h5ad\]](https://ndownloader.figshare.com/files/33979517) [\[curation nb\]](https://nbviewer.ipython.org/github/theislab/sc-pert/blob/main/datasets/Srivatsan_2019_sciplex2_curation.ipynb) [\[curation nb\]](https://nbviewer.ipython.org/github/theislab/sc-pert/blob/main/datasets/Srivatsan_2019_curation.ipynb) [\[processing nb\]](https://nbviewer.ipython.org/github/theislab/sc-pert/blob/main/datasets/Srivatsan_2019_sciplex3.ipynb),small molecules,188,3,4,2,"650,000",Human,Culture,sci-Plex,GSE139944,,RNA-seq,"Cancer cell lines A549, K562, and MCF7",,"5,000 drug conditions",,3.0,Yes,Yes,No,Yes,No,,,,
9,[Zhao *et al.* bioRxiv](https://doi.org/10.1101/2020.04.22.056341),Deconvolution of Cell Type-Specific Drug Responses in Human Tumor Tissue with Single-Cell RNA-seq,,small molecules,"2,6","6,1",-,-,"48,404",Human,"Brain, Tumor",SCRB-seq (microwell),GSE148842,,RNA-seq,,,,,,,,,,,,,,6.0
12,[McFarland *et al.* NCommunications](https://doi.org/10.1038/s41467-020-17440-w),Multiplexed single-cell transcriptional response profiling to define cancer vulnerabilities and therapeutic mechanism of action, [\[curation nb\]](https://nbviewer.ipython.org/github/theislab/sc-pert/blob/main/datasets/McFarland_2020_curation.ipynb) [\[processing nb\]](https://nbviewer.ipython.org/github/theislab/sc-pert/blob/main/datasets/McFarland_2020.ipynb),small molecules,1-13,24-99,1,1-5,,Human,Culture,MIX-seq,,,RNA-seq,,,,,,,,,,,,,,
22,[Chen *et al.* (2020)](https://doi.org/10.1038/s41592-019-0689-z),,,small molecules,300,1,1,1,,,,CyTOF,,,protein,breast  cancer  cells  undergoing  TGF-β-induced  EMT ,,,,,,,,,,,,,