Single-cell decoding of drug induced transcriptomic reprogramming in triple negative breast cancers

Table 1 Types and numbers of single-cell RNA-seq data generated for this study

Current label of TNBC PDX	Previous label [26, 29]	Condition	No. of scRNA-seq passages	No. of scRNA-seq cells sequenced	No. of filtered cells for analysis	Percentage of cells assigned to clones
Pt1	SA501	Untreated (UnRx)	1	7,799	2,600	75.9%
Pt2	SA530	Untreated (UnRx)	1	3,021	1,207	94.6%
Pt3	SA604	Untreated (UnRx)	3	7,369	3,685	84.6%
Pt4	SA609	Untreated (UnRx)	5	22,628	12,109	99.9%
		Cisplatin (Rx)	4	12,281	8,001	100%
		Cisplatin holiday (RxH)	3	9,857	6,828	100%
Pt5	SA535	Untreated (UnRx)	5	9,076	4,371	99.9%
		Cisplatin (Rx)	4	7,551	3,322	94.4%
		Cisplatin holiday (RxH)	3	5,801	2,284	96.8%
Pt6	SA1035	Untreated (UnRx)	5	16,803	4,104	76%
		Cisplatin (Rx)	4	10,970	2,788	80.6%
		Cisplatin holiday (RxH)	3	9,147	2,344	98.0%
Total untreated Pt1-Pt6		Untreated (UnRx)	20	66,696	28,074	92%
Total Cisplatin Pt4-Pt6		Cisplatin (Rx)	12	30,802	14,111	95%
Total Cisplatin-hol iday Pt4-Pt6		Cisplatin holiday (RxH)	9	24,805	11,456	98.9%
Total Pt1-Pt6		All conditions	41	126,556	53,641	94.2%

The columns show: (1) the patient label Pt1-6; (2) the previous labels used in other publications; (3) the treatment conditions: untreated, treated with cisplatin and treated with cisplatin followed by holiday; (4) the number of scRNA-seq passages; (5) the number of scRNA-seq cells initially sequenced; (6) the number of cells after applying the mouse contamination, quality control and doublet filters (see Methods)—all these cells were used as input to clonealign and in the pseudotime analysis; (7) the percentage of cells that were assigned to clones by clonealign after additional filtering and clone assignment (see Methods). See Additional file 2: Table S1 for details of each individual sample

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