Dual RNA-seq reveals no plastic transcriptional response of the coccidian parasite Eimeria falciformis to host immune defenses

Ehret, Totta; Spork, Simone; Dieterich, Christoph; Lucius, Richard; Heitlinger, Emanuel

doi:10.1186/s12864-017-4095-6

Table 1 Summary of data per sample, sorted according to number of reads mapping to the E. falciformis genome

From: Dual RNA-seq reveals no plastic transcriptional response of the coccidian parasite Eimeria falciformis to host immune defenses

Sample^a	Sequencing method	Batch	Total reads	Reads mapping mouse	Reads mapping E. falciformis	Percentage E. falciformis	# E. falciformis genes^b
NMRI_2ndInf_0dpi_rep1	GAII	2	108,937,797	70,489,674	247	0.0004	1
Rag_1stInf_0dpi_rep1	hiseq	3	25,362,793	18,853,850	443	0.0023	2
C57BL/6_1stInf_0dpi_rep1	hiseq	3	35,731,249	25,119,348	457	0.0018	2
C57BL/6_1stInf_0dpi_rep2	hiseq	3	47,085,959	34,377,133	608	0.0018	2
Rag_1stInf_0dpi_rep2	hiseq	3	46,556,156	35,233,327	676	0.0019	2
NMRI_2ndInf_0dpi_rep2	hiseq	3	58,122,244	40,794,245	3406	0.0083	51
NMRI_2ndInf_3dpi_rep1^c	hiseq	3	57,934,016	40,544,287	4803	0.0118	95
NMRI_2ndInf_5dpi_rep2^c	hiseq	3	63,965,539	48,289,181	10,941	0.0227	407
NMRI_1stInf_0dpi_rep1^c	GAII	1	82,364,585	55,176,243	17,954	0.0325	701
NMRI_2ndInf_3dpi_rep2	hiseq	3	65,548,826	46,171,909	29,548	0.0640	1580
NMRI_2ndInf_7dpi_rep2	hiseq	3	67,487,466	51,722,265	40,091	0.0775	1836
Rag_1stInf_5dpi_rep1	hiseq	3	38,651,359	29,982,453	63,024	0.2098	2548
Rag_1stInf_5dpi_rep2	hiseq	3	34,779,832	25,297,803	99,000	0.3898	2828
C57BL/6_1stInf_5dpi_rep1	hiseq	3	40,904,388	29,319,604	185,969	0.6303	4173
Rag_2ndInf_5dpi_rep1	hiseq	3	50,049,848	37,093,621	192,856	0.5172	4167
C57BL/6_1stInf_5dpi_rep2	hiseq	3	29,511,368	18,062,349	215,696	1.1801	3823
C57BL/6_2ndInf_5dpi_rep1	hiseq	3	35,148,432	25,660,184	262,909	1.0142	4563
NMRI_1stInf_3dpi_rep1	GAII	1	73,236,430	49,993,358	394,384	0.7827	5220
NMRI_1stInf_3dpi_rep2	GAII	2	160,709,694	117,791,044	413,051	0.3494	4862
NMRI_1stInf_5dpi_rep2	GAII	2	119,902,722	76,419,774	794,570	1.0290	5333
NMRI_2ndInf_5dpi_rep1	GAII	2	230,773,955	143,186,486	1,846,840	1.2734	5533
NMRI_2ndInf_7dpi_rep1	hiseq	3	70,366,762	41,467,146	8,634,201	17.2335	5875
NMRI_1stInf_5dpi_rep1	GAII	2	76,702,168	47,037,087	8,669,701	15.5631	5700
Sporozoites_rep2	GAII	0	19,551,681	8656	11,470,604	99.9246	5513
NMRI_1stInf_5dpi_rep3	GAII	0	191,099,180	83,735,624	27,839,458	24.9513	5784
NMRI_1stInf_7dpi_rep1	GAII	1	66,505,514	3,310,666	39,400,884	92.2488	5932
Sporozoites_rep1	GAII	1	67,325,397	4334	43,774,401	99.9901	5825
Oocysts_rep1	GAII	1	68,859,802	3805	49,653,065	99.9923	5695
Oocysts_rep2	GAII	0	151,090,783	18,524	71,019,860	99.9739	5777
NMRI_1stInf_7dpi_rep2	GAII	1	139,749,046	21,699,324	73,539,445	77.2159	5943

^aSample names are given with information separated by underscore as follows: 1) mouse strain, 2) naïve (1^st) or challenge (2^nd) infection, 3) dpi (days post infection), and 4) replicate number
^bNumber of expressed E. falciformis genes (read counts >5)
^cThese samples were removed from downstream analyses because of uncertain infection status

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ISSN: 1471-2164

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