Small RNA fragments derived from multiple RNA classes – the missing element of multi-omics characteristics of the hepatitis C virus cell culture model

Jackowiak, Paulina; Hojka-Osinska, Anna; Philips, Anna; Zmienko, Agnieszka; Budzko, Lucyna; Maillard, Patrick; Budkowska, Agata; Figlerowicz, Marek

doi:10.1186/s12864-017-3891-3

Table 3 Features of the 26 representative RNA fragments with log₂FC > 5^a

From: Small RNA fragments derived from multiple RNA classes – the missing element of multi-omics characteristics of the hepatitis C virus cell culture model

Sequence	Length	Parental RNA	RNA class	Fragment type	log₂FC 72 hpi^b	log₂FC 96 hpi^b	Relative abundance
Sequence	Length	Parental RNA	RNA class	Fragment type	log₂FC 72 hpi^b	log₂FC 96 hpi^b	72C	72I	96C	96I
AAACUCGACUGCAUAAUUUGUGGUAGUGGGGGACUG	36	U1 spliceosomal RNA	snRNA	Sm binding	5.14	11.59	0.00%	0.01%	0.00%	0.26%
AUGUGGGAAACUCGACUGCAUAAUUUGUGGUAGUGGGGGA	40	U1 spliceosomal RNA	snRNA	Sm binding	7.27	11.33	0.00%	0.01%	0.00%	0.21%
AAUGUGGGAAACUCGACUGCAUAAUUUGUGGUAGUGGGGGACU	43	U1 spliceosomal RNA	snRNA	Sm binding	8.36	9.93	0.00%	0.34%	0.00%	3.09%
ACCCCACGUCUCGUCGCG	18	FGF-2 internal ribosome entry site (IRES)	other	n/a^c	6.54	9.45	0.00%	0.04%	0.00%	0.26%
GGUCCGCCGGCCCUG	15	Putative conserved non-coding region (EvoFold)	other	n/a	6.90	9.35	0.00%	0.05%	0.00%	0.27%
AAACUCGACUGCAUAAUUUGUGGUAGUGGGGGACU	35	U1 spliceosomal RNA	snRNA	Sm binding	5.70	9.02	0.01%	0.40%	0.01%	5.00%
ACUCGACUGCAUAAUUUGUGGUAGUGGGGGACUG	34	U1 spliceosomal RNA	snRNA	Sm binding	5.67	9.00	0.00%	0.19%	0.01%	2.55%
AUGUGGGAAACUCGACUGCAUAAUUUGUGGUAGUGGGG	38	U1 spliceosomal RNA	snRNA	Sm binding	6.71	8.92	0.00%	0.25%	0.01%	2.89%
CUGGCAGGGGAGAUACCAUGAUCACGAAGGUGGUUUUCCCAGGGC	45	U1spliceosomalRNA	snRNA	no functional region	6.49	8.45	0.00%	0.07%	0.00%	0.93%
GAGUUCUGGGCUGUAGUGCGCU	22	7S RNA	other	n/a	4.67	8.33	0.00%	0.06%	0.00%	0.29%
UGGGCAGGAGAUGCCGUGGACCCC	24	Nuclear RNase P	other	n/a	5.22	8.18	0.00%	0.03%	0.00%	0.29%
UCACCCGGCCCGGACACG	18	piRNA	other	n/a	5.07	8.18	0.01%	0.34%	0.01%	4.13%
GGGACUGACCUGAAAUGAAGAGAAUACU	28	C/D box snoRNA, SNORD2/snR39B	snoRNA	box D’	4.20	7.88	0.00%	0.02%	0.00%	0.30%
ACUCGACUGCAUAAUUUGUGGUAGUGGGG	29	U1 spliceosomal RNA	snRNA	Sm binding	5.22	7.82	0.02%	0.58%	0.03%	7.43%
AUUGCACUCCGGAUGUGCUGACCCCU	26	U1 spliceosomal RNA	snRNA	no functional region	4.88	6.87	0.00%	0.06%	0.00%	0.46%
AUUGCACUCCGGAUGUGCUGACCCCUGCGAUUUCCCCAAAUGUGG	45	U1 spliceosomal RNA	snRNA	no functional region	4.21	6.49	0.00%	0.04%	0.00%	0.26%
UCACCCGGCCCGGAC	15	piRNA	other	n/a	5.02	6.31	0.01%	0.25%	0.02%	1.76%
ACCCAGGCGGCCCGGGUUCGACUCCCGGUGUG	32	tRNA, TTC (Glu)	tRNA	tRF-Δ5A-Δ3AA	5.62	6.14	0.00%	0.04%	0.00%	0.30%
GCGCGCCGGCCGGGCG	16	Putative conserved non-coding region (EvoFold)	other	n/a	4.26	5.69	0.01%	0.26%	0.04%	1.89%
UUUUACGGAUCUGGCUUCUGAGA	23	C/D box snoRNA, SNORD50/U50A	snoRNA	box D, guide sequence	1.36	5.65	0.03%	0.07%	0.01%	0.57%
CACGCAUCGACCUGGUAUUGCAGUACCUCCAGGAACGG	38	U2 spliceosomal RNA	snRNA	no functional region	2.62	5.47	0.05%	0.31%	0.04%	1.78%
UAGCUCUAGAAUUACUCUGAGACCU	25	C/D box snoRNA, SNORD45/U45	snoRNA	box D	0.90	5.30	0.03%	0.05%	0.01%	0.31%
AUACAUGAUGAUCUCAAUCCAACUUGAACUCU	32	C/D box snoRNA, SNORD81/U81/Z23	snoRNA	box C	2.82	5.13	0.01%	0.06%	0.01%	0.34%
AAUCUGUAGUCUUGGAGCCGCACAGGGUUGGUGGUACCCUCG	42	scaRNA, scaRNA13/U93	snoRNA	no functional region	1.72	5.11	0.03%	0.11%	0.02%	0.85%
ACUUUAGCUCUAGAAUUACUCUGAGACCU	29	C/D box snoRNA, SNORD45/U45	snoRNA	box D, guide sequence	2.00	5.05	0.09%	0.35%	0.06%	2.14%
AGAAAUAUGUCUGAUAAAAGAUUUACUUUGAUAGAGUAAAUAAUAGGAGCU	51	tRNA, GAT (Ile)	tRNA	tRF-5T	1.47	5.00	0.02%	0.07%	0.01%	0.33%

^aat least at 96 hpi (FDR < 0.05; sorted by log₂FC at 96 hpi)
^bdifferentially accumulated are marked with boldtype
^cnot applicable

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