A fast and cost-effective microsampling protocol incorporating reduced animal usage for time-series transcriptomics in rodent malaria parasites

Table 1 Microsample characteristics and RNA-seq mapping statistics

RMP	Microsample	Parasitaemia	RNA yield (μg)	Total reads	Parasite reads	Mapping percentage	Median fragment coverage	Median TIN
P. chabaudi	Sample I	7.74	0.87	26,585,563	1,228,998	4.62	8	87.66
	Sample II	6.22	0.42	19,842,987	2,458,755	12.39	49	86.41
	Sample III	5.75	1.71	15,332,092	676,488	4.41	10	92.2
	Sample IV	3.64	1.03	31,385,250	1,420,373	4.52	26	91.13
P. vinckei	6h_rep1	23.88	9.6	32,755,140	22,915,171	69.96	499	91.27
	6h_rep2	22.19	9	31,427,694	21,274,632	67.69	479	91.15
	6h_rep3	23.14	9.03	31,331,956	20,044,950	63.98	424	91.04
	12h_rep1	24.19	11.49	35,255,928	26,290,657	74.57	710.5	91.79
	12h_rep2	24.32	11.46	28,504,674	16,567,841	58.12	451.5	86.61
	12h_rep3	22.75	10.14	27,368,020	17,521,494	64.02	483.5	92
	18h_rep1	24.77	6.33	27,622,130	18,733,720	67.82	582	89.88
	18h_rep2	25.65	11.49	29,253,240	18,590,556	63.55	552	91.11
	18h_rep3	23.11	10.23	27,377,938	15,234,884	55.65	468	90.08
	24h_rep1	27.06	5.4	33,624,482	25,522,094	75.90	698	91.57
	24h_rep2	25.92	1.24	35,255,928	20,282,255	57.53	501.5	87.43
	24h_rep3	26.45	1.95	35,255,928	23,045,897	65.37	634	90.69

Microsamples from Plasmodium chabaudi AS had low parasitaemia and therefore, a low percentage of reads mapping to the P. chabaudi genome. In contrast, Plasmodium vinckei vinckei CY microsamples had lesser host contamination resulting in higher median fragment coverage across its transcripts. Transcript integrity number (TIN) was calculated using RSeQC [51] and all samples showed a high TIN value, indicating little to no evidence of RNA degradation