The Use of MPSS for Whole-Genome Transcriptional Analysis in Arabidopsis

Table 1.

Libraries and MPSS Signature Summary Statistics

#
Library
Code
2-step runs
2-step signatures
4-step runs
4-step signatures
Total signatures
Total distinct signatures
Total distinct, significant, reliable
A. 17-base MPSS signature data
1 Callus CAFa 2 1,014,442 2 945,097 1,959,539 40,901 20,081
2 Inflorescence INFa 3 1,137,173 2 637,133 1,774,306 37,750 18,367
3 Leaves LEFa 3 1,364,617 3 1,519,981 2,884,598 53,394 20,465
4 Roots ROFa 5 2,340,375 3 1,302,257 3,642,632 48,100 20,713
5 Silique SIFa 2 980,274 2 1,032,585 2,012,859 38,501 19,714
6 apt1-10 Inflor. AP1 2 1,290,799 2 1,673,925 2,964,724 61,270 22,454
7 ap3-6 Inflor. AP3 2 1,097,876 2 1,338,089 2,435,965 52,172 25,229
8 agamous Inflor. AGM 2 1,058,093 2 1,517,577 2,575,670 41,091 17,488
9 Inflorescence-2 INS 2 1,315,770 2 1,575,124 2,890,894 53,982 22,347
10 Roots-2 ROS 2 1,247,698 2 1,210,738 2,458,436 43,728 22,274
11 sup/ap1-10 Inflor. SAP 2 1,061,249 2 1,249,101 2,310,350 38,002 20,836
12 SA 4 hr—leaf S04 2 1,469,036 2 1,537,939 3,006,975 21,701 11,374
13 SA 52 hr—leaf S52 2 1,476,603 2 1,488,237 2,964,840 24,213 12,628
14 Leaves-2 LES 2 1,562,225 2 1,547,160 3,109,385 44,086 22,525
Total 33 18,416,230 30 18,574,943 36,991,173 268,132b 87,705b
B. 20-base MPSS signature data
1 Callus CAFa 2 832,604 2 804,803 1,637,407 35,284 19,542
2 Inflorescence INFa 3 933,710 2 522,137 1,455,847 31,561 17,271
3 Leaves LEFa 3 1,144,721 3 1,313,015 2,457,736 46,113 18,320
4 Roots ROFa 5 1,897,860 3 1,104,358 3,002,218 41,225 19,660
5 Silique SIFa 2 808,348 2 865,560 1,673,908 32,474 17,614
6 ap1-10 Inflor. AP1 2 1,087,743 2 1,471,249 2,558,992 57,404 21,731
7 ap3-6 Inflor. AP3 2 892,242 2 1,158,405 2,050,647 48,644 22,050
8 agamous Inflor. AGM 2 867,439 2 1,298,189 2,165,628 34,950 15,543
9 Inflorescence-2 INS 2 1,119,870 2 1,396,268 2,516,138 50,839 23,059
10 Roots-2 ROS 2 1,020,885 2 1,026,684 2,047,569 38,015 21,457
11 sup/ap1-10 Inflor. SAP 2 835,574 2 1,038,723 1,874,297 33,026 19,615
12 SA 4 hr—leaf S04 2 1,277,278 2 1,349,668 2,626,946 18,787 10,557
13 SA 52 hr—leaf S52 2 1,276,762 2 1,308,033 2,584,795 21,381 11,962
14 Leaves-2 LES 2 1,378,453 2 1,373,972 2,752,425 41,218 22,495
Total
33
15,373,489
30
16,031,064
31,404,553
238,311b
84,262b

  • ↵a Sequenced by “classic” MPSS method.

  • ↵b Calculated as the union of the set of all libraries.

This Article

  1. Genome Res. 14: 1641-1653

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