Co-expression network analysis of duplicate genes in maize (Zea mays L.) reveals no subgenome bias

Li, Lin; Briskine, Roman; Schaefer, Robert; Schnable, Patrick S.; Myers, Chad L.; Flagel, Lex E.; Springer, Nathan M.; Muehlbauer, Gary J.

doi:10.1186/s12864-016-3194-0

Table 1 Transcriptome Datasets used in our study

From: Co-expression network analysis of duplicate genes in maize (Zea mays L.) reveals no subgenome bias

ID	Tissues/Stages	Tissue classification	# Total reads	% contaminating adaptor sequences	% bases >q20	Uniquely mapped reads in FGS gene space	% reads in FGS gene space	Reference
1	Trans	SAM related - embryo	22994564	5.24	95.87	17664753	76.82	[63]
2	LM	SAM related - LM	33567585	3.66	97.70	18748653	55.85	[63]
3	L1	SAM related - embryo	39027020	2.11	98.14	25877026	66.31	[63]
4	L14	SAM related - embryo	31676873	3.31	98.10	24636049	77.77	[63]
5	Col	SAM related - embryo	41066790	2.95	98.05	27532949	67.04	[63]
6	V5_Shoot_tip	SAM containing	37966015	5.49	96.71	31957110	84.17	[45]
7	V3_Stem and SAM	SAM containing	75700900	7.24	90.86	58077428	76.72	[45]
8	V1_4D_PE_Stem_SAM	SAM containing	68096357	5.66	95.80	58736028	86.25	[45]
9	V5_First_elonagetd_internode	stem	50620425	5.42	96.78	42021210	83.01	[45]
10	V9_Fourth_elongated_internode	stem	49883803	4.68	96.64	42811552	85.82	[45]
11	V1_4D_PE_Primary_root	root	34338211	5.38	96.03	28431679	82.80	[45]
12	6DAS_GH_Primary Root	root	75974682	7.89	94.81	58789326	77.38	[45]
13	tassel_stg1	tassel	41685877	1.38	99.38	37715842	90.48	[64]
14	tassel_stg3	tassel	44907570	1.60	99.08	39810029	88.65	[64]
15	tassel_stg2	tassel	33527176	1.28	98.97	29884294	89.13	[64]
16	R1_Anthers	tassel	50390993	6.51	95.22	42255501	83.86	[45]
17	V13_Immature_tassel	tassel	67777936	4.83	96.86	57328334	84.58	[45]
18	V18_Meiotic_tassel	tassel	90322080	4.17	96.99	76409461	84.60	[45]
19	V18_Immature_cob	ear	63065877	4.27	96.92	51946957	82.37	[45]
20	ear_tip	ear	19469355	3.85	97.91	17259171	88.65	[64]
21	ear_mid	ear	22832854	1.66	98.69	20181747	88.39	[64]
22	ear_base	ear	22257472	2.06	99.34	19599692	88.06	[64]
23	R1_Pre-pollination_cob	ear	78890387	3.61	97.56	65827854	83.44	[45]
24	R1_Silks	ear	85297444	3.47	97.73	73722387	86.43	[45]
25	16DAP_Whole_seed	seed	36090184	5.88	96.18	30262739	83.85	[45]
26	24H_Germinating Seed	seed	67115301	9.53	93.24	50590975	75.38	[45]
27	14DAP_Whole_seed	seed	57197138	8.00	94.15	49994899	87.41	[45]
28	10DAP_Whole_seed	seed	59980127	6.77	95.05	51983114	86.67	[45]
29	12DAP_Whole_seed	seed	55057984	7.51	94.26	47658798	86.56	[45]
30	18DAP_Pericarp	seed	45315693	8.06	94.50	37642629	83.07	[45]
31	2DAP_Whole_seed	seed	50626444	7.31	94.38	43151312	85.23	[45]
32	18DAP_Whole_Seed	seed	54296830	9.77	92.49	47308022	87.13	[45]
33	6DAP_Whole_seed	seed	53677071	10.33	92.65	45188276	84.19	[45]
34	8DAP_Whole_Seed	seed	58148634	10.14	92.10	48258631	82.99	[45]
35	20DAP_Whole_Seed	seed	76914729	7.66	94.53	60236045	78.32	[45]
36	22DAP_Whole_Seed	seed	71960325	8.36	93.25	61230630	85.09	[45]
37	24DAP_Whole_Seed	seed	92168996	7.53	94.03	80572513	87.42	[45]
38	4DAP_Whole_Seed	seed	100145919	8.22	93.97	84635434	84.51	[45]
39	14DAP_Endosperm	endosperm	47165528	5.74	95.93	41130552	87.20	[45]
40	16DAP_Endosperm	endosperm	43133667	24.17	81.93	36465697	84.54	[45]
41	24DAP_Endosperm	endosperm	44105309	6.98	95.06	39097597	88.65	[45]
42	22DAP_Endosperm	endosperm	50805946	8.39	93.89	44051966	86.71	[45]
43	20DAP_Endosperm	endosperm	73033574	8.58	93.76	56588796	77.48	[45]
44	18DAP_Endosperm	endosperm	71722169	9.68	92.92	62724952	87.46	[45]
45	12DAP_Endosperm	endosperm	105002559	3.78	97.71	90746296	86.42	[45]
46	Pro	embryo	29413276	4.14	96.73	12517310	42.56	[63]
47	16DAP_Embryo	embryo	42474548	25.27	81.01	35238795	82.96	[45]
48	20DAP_Embryo	embryo	46773334	8.18	93.69	39847251	85.19	[45]
49	22DAP_Embryo	embryo	54593430	8.38	94.22	46407023	85.00	[45]
50	18DAP_Embryo	embryo	66441077	8.93	93.22	55947651	84.21	[45]
51	24DAP_Embryo	embryo	69915678	7.27	94.61	59151359	84.60	[45]
52	VT_Thirteenth_Leaf	leaf	37375422	14.22	88.85	28643636	76.64	[45]
53	V9_Eleventh_Leaf	leaf	34439420	9.38	92.76	29562400	85.84	[45]
54	R2_Thirteenth_Leaf	leaf	44695525	11.87	91.31	35886544	80.29	[45]
55	V9_Thirteenth_Leaf	leaf	44205877	14.04	89.31	36100685	81.66	[45]
56	V9_Eighth_Leaf	leaf	50771168	13.85	89.38	42468259	83.65	[45]
57	V9_Immature_Leaves	leaf	43514876	25.26	81.13	35013880	80.46	[45]
58	V1_4D_PE_Pooled_Leaves	leaf	52523629	8.80	93.61	44510623	84.74	[45]
59	V3_Topmost_leaf	leaf	55571667	6.22	96.08	46448356	83.58	[45]
60	V7_Bottom_of_transition_leaf	leaf	53754587	5.08	96.09	46018705	85.61	[45]
61	V5_Bottom_of_transition_leaf	leaf	62309853	5.04	97.24	53863310	86.44	[45]
62	V5_Tip of stage-2 Leaf	leaf	79560349	6.88	94.70	63185974	79.42	[45]
63	V7_Tip_of_transition_leaf	leaf	84671628	5.19	95.87	71020587	83.88	[45]
64	6_DAS_GH_Coleoptile	leaf	121128249	6.43	94.92	103474057	85.43	[45]

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