Identification and characterization of miRNAs in the gills of the mud crab (Scylla paramamosain) in response to a sudden drop in salinity

Wang, Huan; Wei, Hongling; Tang, Lei; Lu, Junkai; Mu, Changkao; Wang, Chunlin

doi:10.1186/s12864-018-4981-6

Table 4 miRNA expression in the LS and CK groups

From: Identification and characterization of miRNAs in the gills of the mud crab (Scylla paramamosain) in response to a sudden drop in salinity

ID	Sequence	Read count		log₂Ratio (LS/CK)	Up / down	P_ value	Q _ value	Different expression
ID	Sequence	CK	LS	log₂Ratio (LS/CK)	Up / down	P_ value	Q _ value	Different expression
novel_mir1	AAGAGAGCUAUCCGUCGACAGU	11,244,923	9,582,299	−0.12	down	0	0	No
miR-100-5p_1	AACCCGUAGAUCCGAACUUGU	5,794,803	6,054,139	0.18	up	0	0	No
miR-100-5p	AACCCGUAGAUCCGAACUUGUG	2,939,724	2,764,103	0.03	up	1.68E-127	1.02E-128	No
miR-100	AACCCGUAGAUCCGAACUU	326,542	343,837	0.19	up	0	0	No
novel_mir2	AUAGGUAGCUCUGAGUCCAGAG	217,367	216,078	0.11	up	1.4E-133	9.19E-135	No
novel_mir3	UACUGGCCUGCUAAGUCCCAAG	105,094	113,448	0.23	up	2.12E-295	2.58E-296	No
novel_mir4	UCCCUGAGACCCUUUCUUGUGA	45,082	50,918	0.29	up	3.49E-215	2.97E-216	No
novel_mir8	AAAUAUCAGCUGGUAAAUUUGG	23,653	28,276	0.37	up	1.1E-190	7.78E-192	No
novel_mir5	CAAUGCCCUUGGAAAUCCCAAA	55,060	25,181	−1.01	down	0	0	Yes
miR-7a	UGGAAGACUAGUGAUUUUGUUGUU	22,817	23,572	0.16	up	5.26E-34	2.49E-35	No
novel_mir7	AGAUGACUACACGGCUGUGAGA	67,340	20,469	−1.60	down	0	0	Yes
novel_mir6	UGACUAGAGAUUCACACUCAUCC	17,884	18,990	0.20	up	2.25E-41	1.2E-42	No
novel_mir29	UGAACACAGCUGGUGGUAUCU	14,482	18,625	0.48	up	5.76E-199	4.45E-200	No
miR-7a_1	UGGAAGACUAGUGAUUUUGUUGU	12,463	11,125	−0.05	down	0.010473726	0.00024088	No
novel_mir9	CUUACGACCGCCUAGCACGGUA	8913	8789	0.10	up	0.0000104	2.77E-07	No
miR-7_2	UGGAAGACUAGUGAUUUUGUU	14,450	8319	−0.68	down	7.7E-268	8.19E-269	No
novel_mir10	GUACCGAAGCUGCGGAUGCGU	4672	8016	0.89	up	4.01E-258	3.79E-259	No
miR-7	UGGAAGACUAGUGAUUUUGUUG	1157	6374	2.58	up	0	0	Yes
novel_mir11	UGAGAGUGAGAGAUAGAGAGGA	5282	5626	0.21	up	7.06E-14	2.86E-15	No
novel_mir46	UGAUACUCGGGUGCCUGUUC	1227	1642	0.54	up	4.03E-23	1.81E-24	No
novel_mir56	GGUGUAGCAUAAGUGGGA	1384	975	−0.39	down	7.45E-11	2.75E-12	No
novel_mir39	UCUCCUCUUCCACUUUCUCGUC	245	415	0.88	up	1.71E-14	7.28E-16	No
novel_mir42	GUACAUGAGUUUGGGGAGGAUG	412	410	0.11	up	0.279773023	0.00529043	No
novel_mir12	AGAGGAAGCACAGGAUGAAGCA	299	321	0.23	up	0.059704709	0.00123915	No
novel_mir16	GCACCGAAGCUUAGGGUUCAGA	31	247	3.11	up	3.65E-46	2.07E-47	Yes
novel_mir13	UGAGGGGAAUGUGUUGGCCAGU	211	205	0.07	up	0.600140943	0.01063922	No
novel_mir34	UCACAGCCGUGUAGUCAUCUUG	536	172	−1.52	down	9.21E-39	4.61E-40	Yes
novel_mir38	UAACGUUUCGUACAGAGUACUU	86	156	0.97	up	0.000000268	8.45E-09	No
novel_mir25	CCUAUCACCACUACCACUACUG	118	106	−0.04	down	0.839846761	0.01429315	No
novel_mir17	UGGUGGCUGGUCGAGCGAGGACU	62	72	0.33	up	0.184002039	0.00369166	No
novel_mir21	UGGAGGAUGGAAGGCCGUGUGU	74	54	−0.34	down	0.186548791	0.00369166	No
novel_mir27	GUCGAGGAGAGGUCAGUGCCA	28	50	0.95	up	0.004289186	0.00010138	No
novel_mir47	AUGAUGGCAGCGGUGACUCGA	0	43	6.54	up	4.94E-12	1.91E-13	Yes
novel_mir36	ACGGGUGGAUGGGUGGGUG	37	43	0.33	up	0.303079488	0.00560656	No
novel_mir50	CGGGAGAGUUAAUUAGCAGUGUU	65	41	−0.55	down	0.053070425	0.00112899	No
novel_mir22	UGAGGGUGACUGGCAGGUGU	0	32	6.12	up	0.000000002	6.82E-11	Yes
novel_mir26	AUGAUGGCAGCGGUGACUCGA	14	28	1.12	up	0.014920708	0.00033412	Yes
novel_mir40	UGGAAUGCAUGGCUACACUUCAGU	0	27	5.87	up	3.44E-08	1.12E-09	Yes
novel_mir53	GGGUUAGUCGGGUCCUAAG	14	27	1.06	up	0.021514563	0.00046942	Yes
novel_mir49	UUGGCUGAUCCAGUAAGUUGU	40	27	−0.45	down	0.2046118	0.00395709	No
novel_mir35	UGUAUUGGGCGUGUGUUGGCCA	0	23	5.64	up	0.000000354	1.08E-08	Yes
novel_mir18	UAUAAUGGCUAUUGGUAUUCU	0	14	4.92	up	0.0000862	0.00000222	Yes
novel_mir20	UGACGGCGCCGCCACUACUGCU	17	14	−0.16	down	0.75159718	0.0130523	No
novel_mir19	AUCCUUGGACCACAGCAGAUGC	0	12	4.70	up	0.000309356	0.00000774	Yes
novel_mir37	CGCAGAUCCAGAAUGUUCCUCA	37	12	−1.51	down	0.000684211	0.0000166	Yes
novel_mir41	CGUGGGCAGGUGUGGGUGGCU	16	12	−0.30	down	0.584887298	0.01058942	No
novel_mir45	GGCGUGGCAGGGGUUUCUCGGACA	37	0	−6.09	down	5.77E-10	2.04E-11	Yes
novel_mir24	UCACCACUCUUGUCUCUGCCGAA	24	0	−5.47	down	0.0000006	1.76E-08	Yes
novel_mir48	UUACCCUGAUAUUCCUUGCCUGU	23	0	−5.41	down	0.00000105	2.96E-08	Yes
novel_mir31	CUAAUUUGAGCCAUCUGUCAGU	21	0	−5.28	down	0.0000032	8.79E-08	Yes

RNA sequencing was conducted as a random sampling process, in which each read was sampled independently and uniformly from every possible nucleotide in the sample [16]. Under this assumption, the number of reads of a single gene (or transcript isoform) follows a binomial distribution (and can be approximated by a Poisson distribution). Screening differentially expressed small RNAs [45] proposes a novel method based on the MA-plot, which is a statistical analysis tool having been widely used to detect and visualize the intensity-dependent ratio of microarray data [51]. ID: miRNA id; CK: reads count of sample CK; LS: reads count of sample LS; log₂Ratio (LS/CK): Log2 of the difference multiple; Up / down: Up (down) regulated

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ISSN: 1471-2164

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