Characterization of inflammatory factor-induced changes in mesenchymal stem cell exosomes and sequencing analysis of exosomal microRNAs

Table 1 Differentially expressed miRNAs

Top 10 differentially expressed miRNAs
Control group			VCAM-1 group			In the TNFα group			In the IL6 group
sRNA id	Count (16379497)	TPM	sRNA id	Count (23095609)	TPM	sRNA id	Count (20739574)	TPM	sRNA id	Count (32116232)
miR-21-5p	1544110	76933.99	miR-21-5p	1640334	70885.38	miR-21-5p	1454726	70066.87	miR-21-5p	1323387
miR-127-3p	159283	9724.54	miR-127-3p	259830	11250.19	miR-100-5p	408192	19681.79	miR-199a-3p,miR-199b-3p	317377
miR-199a-3p,miR-199b-3p	139220	8499.65	miR-199a-3p, miR-199b-3p	155376	6727.51	miR-127-3p	321306	15492.41	miR-127-3p	300549
miR-100-5p	132865	8111.67	miR-100-5p	140774	6095.27	miR-199a-3p, miR-199b-3p	271902	13110.3	miR-100-5p	265054
miR-222-3p	89564	5468.06	miR-26a-5p	107800	4667.55	miR-23a-3p	140623	6780.42	miR-34a-5p	178542
miR-26a-5p	77524	4732.99	miR-34a-5p	86786	3757.68	miR-222-3p	129932	6264.93	miR-23a-3p	144385
miR-34a-5p	76681	4681.52	miR-451a	77297	3346.83	miR-146a-5p	128078	6175.54	miR-222-3p	111957
miR-181a-5p	67287	4108	miR-23a-3p	71930	3114.44	miR-34a-5p	119952	5783.73	miR-146a-5p	100038
miR-411-5p	56606	3455.91	miR-196a-5p	63939	2768.45	miR-143-3p	101398	4889.11	miR-26a-5p	98114
miR-143-3p	49739	3036.66	miR-181a-5p	62752	2717.05	miR-26a-5p	99628	4803.76	miR-181a-5p	97685

Count is the number of mapped tags, and the value in parentheses is the total number. Transcripts per kilobase million is the standardized expression value. VCAM-1: Vascular cell adhesion molecule-1; TNF: Tumor necrosis factor; IL6: Interleukin 6; TPM: Transcripts per kilobase million.

Table 2 Top 10 differentially expressed miRNAs in each group (Poisson distribution screening)

Comparison of top 10 differentially expressed miRNAs
VCAM-1 group vs control group									TNFα group vs control group									IL6 group vs control group
miRNA id	Count(control)	Count(VCAM-1)	TPM(control)	TPM(VCAM-1)	Log2 ratio(VCAM-1/control)	Up/down-regulation(VCAM-1/control)	P	FDR	miRNA id	Count (control)	Count(TNFα)	TPM (control)	TPM (TNFα)	Log2 ratio(TNFα/control)	Up/down-regulation(TNFα/control)	P	FDR	miRNA id	Count(control)	Count(IL6)	TPM(control)	TPM(IL6)	Log2 ratio(IL6/control)	Up/down-Regulation(IL6/control)	P value	FDR
miR-146a-5p	20510	5173	1252.18	223.98	-2.483	Down	0	0	miR-146a-5p	20510	128078	1252.18	6175.54	2.302123	Up	0	0	miR-3529-3p	473	8930	28.88	278.05	3.267202	Up	0	0
miR-149-5p	4558	2391	278.27	103.53	-1.42644	Down	0	0	miR-342-3p	2117	7130	129.25	343.79	1.411363	Up	0	0	miR-320c	1276	7983	77.9	248.57	1.673957	Up	0	0
miR-222-3p	89564	48444	5468.06	2097.54	-1.38233	Down	0	0	miR-23a-3p	42777	140623	2611.62	6780.42	1.37643	Up	0	0	miR-24-3p	11151	50968	680.79	1586.99	1.221011	Up	0	0
miR-29a-3p	8451	5054	515.95	218.83	-1.23742	Down	0	0	miR-100-5p	132865	408192	8111.67	19681.79	1.278791	Up	0	0	miR-7-5p	16653	101	1016.7	3.14	-8.33891	Down	0	0
miR-451a	2760	77297	168.5	3346.83	4.311975	Up	0	0	miR-337-3p	5655	16027	345.25	772.77	1.162398	Up	0	0	miR-196a-5p	26485	11440	1616.96	356.21	-2.18248	Down	0	0
miR-490-5p	1839	475	112.27	20.57	-2.44836	Down	2.00E-305	1.20E-303	miR-409-3p	4207	11169	256.85	538.54	1.068127	Up	0	0	miR-451a	2760	1658	168.5	51.62	-1.70675	Down	0	0
miR-1246	1812	6191	110.63	268.06	1.276813	Up	1.39E-276	8.02E-275	miR-221-3p	4067	10541	248.3	508.26	1.033482	Up	0	0	miR-379-5p	13430	8083	819.93	251.68	-1.70391	Down	0	0
miR-181a-2-3p	3400	2008	207.58	86.94	-1.25558	Down	2.31E-219	1.18E-217	miR-7-5p	16653	136	1016.7	6.56	-7.27598	Down	0	0	miR-196b-5p	18735	15676	1143.81	488.1	-1.2286	Down	0	0
miR-204-5p	3116	1757	190.24	76.08	-1.32223	Down	3.36E-218	1.66E-216	miR-196a-5p	26485	8359	1616.96	403.05	-2.00425	Down	0	0	miR-424-5p	12774	11917	779.88	371.06	-1.0716	Down	0	0
miR-378e	2	817	0.12	35.37	8.203348	Up	4.36E-186	2.00E-184	miR-26b-5p	6496	3410	396.59	164.42	-1.27026	Down	0	0	miR-26b-5p	6496	6086	396.59	189.5	-1.06545	Down	0	0

P-values were corrected. TPM: Transcripts per kilobase million; FDR: False discovery rate; VCAM-1: Vascular cell adhesion molecule-1; TNF: Tumor necrosis factor; IL6: Interleukin 6.

Table 3 Comparison of differentially expressed angiogenesis-related miRNAs between the TNFα group and control group

miRNA id	Count (control)	Count(TNFα)	TPM (control)	TPM (TNFα)	Log2 ratio (TNFα/ control)	Up/ down-regulation (TNFα/ control)	P	FDR
hsa-miR-196a-5p	26485	8359	1616.96	403.05	-2.004253263	Down	0	0
hsa-miR-320e	161	46	9.83	2.22	-2.14663174	Down	5.95E-23	6.85E-22

P-values were corrected. TPM: Transcripts per kilobase million; FDR: False discovery rate; TNF: Tumor necrosis factor.

Table 4 Comparison of differentially expressed angiogenesis-related miRNAs between the IL6 group and control group

miRNA id	Count (control)	Count (IL6)	TPM (control)	TPM (IL6)	Log2 ratio (IL6/control)	Up/down-regulation (IL6/control)	P	FDR
hsa-miR-196a-5p	26485	11440	1616.96	356.21	-2.182484067	Down	0	0
hsa-miR-17-5p	252	138	15.39	4.3	-1.839584667	Down	2.24E-35	2.98E-34
hsa-miR-146b-5p	78	44	4.76	1.37	-1.79678568	Down	1.08E-11	7.53E-11
hsa-miR-21-3p	440	358	26.86	11.15	-1.268415595	Down	4.66E-35	6.02E-34
hsa-miR-320e	161	153	9.83	4.76	-1.046229843	Down	1.78E-10	1.11E-09

P-values were corrected. TPM: Transcripts per kilobase million; FDR: False discovery rate; IL6: Interleukin 6.