dataset information

barcoding technologies assessed

7 different barcoding technologies We incorporated datasets using FateMap, ClonMapper, SPLINTR, LARRY, CellTag-multi, Watermelon, and TREX barcodes. Each have their own recovery and analysis specifications that we outline in Box 1 of our paper.

Schematic of the structure of different lineage-tracing barcodes, their length, diversity, and fluorescent color. Each barcode contains an expressed fluorescent protein, a unique sequence, known as the barcode, and a polyA tail for capture. The lengths of barcodes in each method are shown as scale bars, and library diversities are shown as circles, sized proportional to their diversity and colored according to fluorescent proteins used.

dataset details

Specifications for barcoded and non-barcoded datasets

Dataset Name	Alias ID	Sample type	Organism	Tissue	Cell line	Genotype	Treatment	Total samples	Publication
	barcoded scRNA-seq datasets
Goyal et al. 1	FM01	Melanoma patient resistant cell line	Homo sapiens	Skin-derived	WM989 A6-G3	BRAF – V600E	Targeted therapy	4	Goyal et al., Nature, 2023 (ref. 28)
Goyal et al. 2	FM02	Melanoma patient resistant cell line	Homo sapiens	Skin-derived	WM989 A6-G3	BRAF – V600E	Targeted therapy	4	Goyal et al., Nature, 2023 (ref. 28)
Goyal et al. 3	FM03	Melanoma patient resistant cell line	Homo sapiens	Skin-derived	WM989 A6-G3	BRAF – V600E	Targeted therapy	2	Goyal et al., Nature, 2023 (ref. 28)
Goyal et al. 4	FM04	Breast cancer patient resistant cell line	Homo sapiens	Breast; mammary gland	MDA-MB-231-D4	BRAF – G464V, KRAS – G13D, TERT – c.1-124C>T, TP53 – R280K	Chemotherapy, cytotoxic	2	Goyal et al., Nature, 2023 (ref. 28)
Goyal et al. 5	FM05	Melanoma patient resistant cell line	Homo sapiens	Skin-derived	WM989 A6-G3	BRAF – V600E	Targeted therapy	2	Goyal et al., Nature, 2023 (ref. 28)
Goyal et al. 6	FM06	Melanoma patient untreated cell line	Homo sapiens	Skin-derived	WM989 A6-G3	BRAF – V600E	No treatment	2	Goyal et al., Nature, 2023 (ref. 28)
Goyal et al. 8	FM08	Primary melanocytes	Homo sapiens	Skin-derived	FOM230-1	WT	No treatment	2	Goyal et al., Nature, 2023 (ref. 28)
Jiang et al.	non_cancer	HIPS differentiation	Homo sapiens	PBMCs	PENN123i-SV20	WT	Cardiac differentiation signal	2	Jiang et al., Genome Biol, 2022 (ref. 31)
Jain et al.	Biorxiv	Stem cell reprogramming	Homo sapiens	Fibroblasts	hiF-T	WT	OKSM	6	Jain et al., Cell Systems, 2024 (ref. 34)
TREX	TREX	neuroepithelial progenitor cells differentiation	Mus musculus	Neural	CD-1		No treatment	4	Ratz et al., Nature neuroscience, 2022 (ref. 37)
LARRY	LARRY, LK	pan-myeloid differentiation	Mus musculus	Blood	Lin-Kit+		cytokines and growth factors	18	Weinreb et al., Science, 2020 (ref. 35)
LARRY	LARRY, LSK	pan-myeloid differentiation	Mus musculus	Blood	Lin-Kit+Sca-1+		cytokines and growth factors	15	Weinreb et al., Science, 2020 (ref. 35)
SPLINTR	SPLINTR_chemo	Acute myeloid leukaemia	Mus musculus	Bone marrow	C57BL/6	MLL-AF9 + KrasG12D	chemotherapy	10	Fennell et al., Nature, 2022 (ref. 26)
SPLINTR	SPLINTR_clone	Acute myeloid leukaemia	Mus musculus	Bone marrow	C57BL/6	MLL-AF9, MLL-AF9 + KrasG12D, MLL-AF9 + Flt3ITD	No treatment	4	Fennell et al., Nature, 2022 (ref. 26)
SPLINTR	SPLINTR_chemoretrans	Acute myeloid leukaemia	Mus musculus	Bone marrow and spleen	C57BL/6	MLL-AF9 + KrasG12D	No treatment	1	Fennell et al., Nature, 2022 (ref. 26)
Watermelon	Watermelon	Breast cancer patient resistant cell line	Homo sapiens	Breast; mammary gland	T-47D	PIK3CA – H1047R; Tp53 – L194F	Targeted therapy	6	This paper
CellTag-multi	CellTag-multi_d	multilineage differentiation (hematopoiesis)	Mus musculus	bone marrow	LSK		cytokines and growth factors	3	Jindal et al., Nature biotechnology, 2023 (ref. 36)
CellTag-multi	CellTag-multi_B4	iEP reprogramming	Mus musculus	embryo	C57BL/6J		EGF	1	Jindal et al., Nature biotechnology, 2023 (ref. 36)
ClonMapper	ClonMapper	CLL resistant cell lines	Homo sapiens	blood	HG3		Chemotherapy	4	Gutierrez et al., Nature Cancer, 2021 (ref. 17)
Smart-seq3	Smart-seq3	neuroepithelial progenitor cells differentiation	Mus musculus	Neural	CD-1		No treatment	2	Mold et al., Cell systems, 2024 (ref. 38)
	nonbarcoded sc-RNA seq datasets
non-barcoded	hm-12k	Synthetic dataset	Homo sapiens, Mus musculus	Human kidney, Murine fibroblasts	HEK293T, NIH3T3	WT	No treatment	1	Zheng et al., Nat Commun, 2017 (ref. 44)
non-barcoded	hm-6k	Synthetic dataset	Homo sapiens, Mus musculus	Human kidney, Murine fibroblasts	HEK293T, NIH3T3	WT	No treatment	1	Zheng et al., Nat Commun, 2017 (ref. 44)
non-barcoded	HMEC-orig-MULTI	HMECs	Homo sapiens	mammary gland	HMEC	WT	No treatment	1	McGinnis et al., Cell Syst., 2019 (ref. 6)
non-barcoded	HMEC-rep-MULTI	HMECs	Homo sapiens	mammary gland	HMEC	WT	No treatment	1	McGinnis et al., Cell Syst., 2019 (ref. 6)
non-barcoded	HEK-HMEC-MULTI	Synthetic dataset	Homo sapiens	Human kidney, mammary gland	HEK293T, HMEC	WT	No treatment	1	McGinnis et al., Cell Syst., 2019 (ref. 6)
non-barcoded	mkidney-ch	Mouse kidney cells	Mus musculus	Mouse kidney	C57BL/6J	WT	No treatment	1	Bernstein et al., Cell Syst., 2020 (ref. 3)
non-barcoded	pbmc-2ctrl-dm	Patient PBMCs	Homo sapiens	Systemic lupus erythematosus (SLE) PBMCs	Patient- derived	Patient- derived	No treatment	1	Kang et al., Nat. Biotechnol., 2018 (ref. 45)
non-barcoded	pbmc-2stim-dm	Patient PBMCs	Homo sapiens	Systemic lupus erythematosus (SLE) PBMCs	Patient- derived	Patient- derived	No treatment	1	Kang et al., Nat. Biotechnol., 2018 (ref. 45)
non-barcoded	cline-ch	Human HEK, K562, KG1, and THP1	Homo sapiens	blood	human - derived	human - derived	No treatment	1	Stoeckius et al., Genome Biol., 2018 (ref. 13)
non-barcoded	pbmc-ch	Human PBMCs	Homo sapiens	blood	human - derived	human - derived	No treatment	1	Stoeckius et al., Genome Biol., 2018 (ref. 13)
non-barcoded	pdx-MULTI	Synthetic dataset	Homo sapiens, Mus musculus	Human breast cancer, mouse immue	PDX mouse model	PDX mouse model	No treatment	1	McGinnis et al., Cell Syst., 2019 (ref. 6)
non-barcoded	nuc-MULTI	Synthetic dataset	Homo sapiens, Mus musculus	nuclei			No treatment	1	McGinnis et al., Cell Syst., 2019 (ref. 6)
	Multiome datasets
ATAC	Watermelon Multiome	Breast cancer patient resistant cell line	Homo sapiens	Breast; mammary gland	MCF7	GATA3 – D336G; PIK3CA – E545K	Targeted therapy	6	This paper

cell types

Stacked bar chart of cell types in all datasets. Each distinct color corresponds to one study, with the proportions of different cell types arranged from most to least prevalent (deepest to lightest) and separated by vertical lines. Adjacent to the bar chart, sketched tissues and cells provide a visualization of the cell types used in the particular study.