Table 2.

Patch-seq datasets with experimental details of each study. Sample size is the number of cells passing QC filters according to the authors (if provided). For studies where we could not find this information we based it on the number of cells available in GEO

Tissue	Species	# Cells	# Donors	Region/Cell types	Assay type	scRNAseq library preparation	Year	Ref	Dataset
Brain	Mouse	58 (10 in vivo)	-	L1 interneurons and pyramidal cells	Acute-slice & In vivo	Smart-seq2-based protocol	2016	Cadwell et al. 2016)	E-MTAB-4092
Brain	Mouse	83	-	L1-2 CCK + interneurons and pyramidal cells	Acute-slice	Smart-seq2-like protocol (STRT-seq/C1)	2016	Fuzik et al. 2016)	GSE70844
Brain	Mouse	41	-	Hippocampal interneurons and pyramidal cells	Acute-slice	SMARTer Ultra Low Input RNA kit	2016	Földy et al. 2016)	GSE75386
Brain	Human	56	-	iPSC-derived neurons	Dispersed cells	SMARTer Ultra Low Input RNA kit	2016	Bardy et al. 2016)	NA
Brain	Human	20	-	iPSC-derived neurons	Dispersed cells	NEBNext Ultra DNA library Prep Kit	2016	Chen et al. 2016)	GSE77564
Brain	Mouse	98	-	interneurons from striatum	Acute-slice	Smart-seq2-like protocol (STRT-seq/C1)	2018	Muñoz-Manchado et al. 2018)	GSE119248
Brain	Mouse	7	-	GABAergic neurons in hippocampus	Acute-slice	SMART-Seq v4 ultra low input RNA kit	2019	Luo et al. 2019)	GSE109755
Brain	Mouse	110	-	L4-5 neurons from neocortex	Acute-slice	SMART-Seq v4 ultra low input RNA kit	2019	Scala et al. 2019)	GSE134378
Brain	Mouse	370a	-	Neural progentior cells in neocortex	Acute-slice	Smart-seq2-based protocol	2019	Ellender et al. 2019)	NA
Brain	Mouse	65	-	apical progenitor cells in neocortex	Acute-slice	SMART-Seq v4 3′ DE Kit	2019	Oberst et al. 2019)	GSE122644
Brain	Mouse	53	-	primary visual cortex	In vivo	Smart-seq2-based protocol	2020	Liu et al. 2020)	GSE115997
Brain	Rat	17	-	CCK + interneurons from hippocampus	Acute-slice	SMART-Seq v4 ultra low input RNA kit	2020	Oláh et al. 2020)	GSE133951
Brain	Mouse	220	-	Cortical neurons	Acute-slice	Smart-seq2-based protocol	2020	Cadwell et al. 2020)	GSE140946
Brain	Mouse	128	-	Parvalbumin-interneurons from hippocampus	Acute-slice	SMART-Seq v4 ultra low input RNA kit	2021	Que et al. 2021)	GSE142546
Brain	Mouse	4,270b	-	Cortical GABAergic interneurons	Acute slice	SMART-Seq v4 ultra low input RNA kit	2020	[101	Brain-Mapf
Brain	Mouse	1,237c	-	primary motor cortex	Acute slice	Smart-seq2-based protocol	2021	109, 111]	BICCNg
Brain	Human	25	11	L5 pyramidal neurons	Acute slice	SMART-Seq v4 ultra low input RNA kit	2021	Kalmbach et al. 2021)	Brain-Mapf
Brain	Human	385	56	L2-3 pyramidal neurons from neocortex	Acute slice	SMART-Seq v4 ultra low input RNA kit	2021	Berg et al. 2021)	Brain-Mapf
Pancreas	Human	1,369	34	Endocrine islet cells and other pancreatic cells	Dispersed cells	Smart-seq2-based protocol	2020	Camunas-Soler et al. 2020)	GSE124742
Pancreas	Human	640d	19	Endocrine islet cells and other pancreatic cells	Dispersed cells	Smart-seq2-based protocol	2022	Dai et al. 2022)	GSE164875
Pancreas	Human	189	3	Cryopreserved endocrine islet cells	Dispersed cells	Smart-seq2-based protocol	2022	Marquez-Curtis et al. 2022)	PancDBh
Pancreas	Mouse	23e	-	Pancreatic β cells	Intact islets	NEBNext single-cell/low input RNA kit	2023	Chabosseau et al. 2023)	NA
Retina	Mouse	472	-	Retinal ganglion cells	Retinal whole-mount	Smart-seq2-based protocol	2022	Huang et al. 2022)	GSE137400

^aFor this study, we inferred the number of cells by adding the information provided across figures

^bAlso a number of macaque (Mayr et al. 2019) and human cells (Mayr et al. 2019)

^cCompanion paper contains 133 (mouse), 6 (macaque), 391 (human)

^dAdditional dataset with > 100 mouse cells

^eThis study uses Ca²⁺ imaging and tagging instead of patch-seq

^fhttps://portal.brain-map.org/explore/classes/multimodal-characterization

^ghttps://www.biccn.org/data

^hhttps://hpap.pmacs.upenn.edu/