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Marie L. Cuvelier, Jian Guo, Alejandra C. Ortiz, Marijke J. van Baren, Muhammad Akram Tariq, Frédéric Partensky, Alexandra Z. Worden
Responses of the picoprasinophyte Micromonas commoda to light and ultraviolet stress
www.plosone.org
www.plosone.org
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257.726 498.3307 m
267.137 498.3307 l
h
f*
269.2913 498.3307 m
278.7024 498.3307 l
h
f*
453.8835 472.3087 m
463.2945 472.3087 l
h
f*
465.4488 472.3087 m
474.8598 472.3087 l
h
f*
237.7134 407.3386 m
242.3622 407.3386 l
h
f*
244.5732 407.3386 m
253.9843 407.3386 l
h
f*
315.2693 381.3165 m
319.9748 381.3165 l
h
f*
322.1291 381.3165 m
331.5402 381.3165 l
h
f*
333.7512 381.3165 m
343.1055 381.3165 l
h
f*
555.4205 224.9008 m
564.9449 224.9008 l
h
f*
347.3575 211.9181 m
561.4866 211.9181 l
h
f*
0 g
1 j
1 J
0 w
10 0 0 10 200.0125 707.4141 cm
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(ceae\))Tj
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0 Tc
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[()-2()22()10()24( )3()7()4()7()1()-4(\r)]TJ
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(22)Tj
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(,)Tj
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(34)Tj
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(].)Tj
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(the)Tj
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[()29()4()1()20()11()6()11()6(\r)]TJ
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[()7()11()18()6()4(\n)4()]TJ
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(and)Tj
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1.7121 0 Td
[()29()4()1()20()]TJ
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[()6()11()6(\r)]TJ
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[()11()-4(\r)10()4()4()4()]TJ
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(one-helix-proteins)Tj
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(\(OHPs\))Tj
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(13)Tj
0 g
(,)Tj
0.83 0.64 0.02 0 k
(34)Tj
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(responses)Tj
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(of)Tj
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(prasinophyte)Tj
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(photosynthetic)Tj
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(and)Tj
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(UV-stress)Tj
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(the)Tj
1.4513 0 Td
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1.2642 0 Td
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(.)Tj
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[()7()11()18()6()4(\n)4()]TJ
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4.0195 0 Td
(\(RCC299\))Tj
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(first)Tj
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[()]TJ
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1.3039 0 Td
[()7()11()18()6()4(\n)4()]TJ
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(the)Tj
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(seven)Tj
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[()29()4()1()20()11()6()11()6(\r)]TJ
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(clades,)Tj
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[()]TJ
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1.3096 0 Td
[()11()-4(\r)10()4()4()4()]TJ
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(belongs)Tj
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([)Tj
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0.83 0.64 0.02 0 k
(30)Tj
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1.7688 0 Td
[()29()4()1()20()11()6()11()6(\r)]TJ
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(a)Tj
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(latitude)Tj
3.1975 0 Td
(environments)Tj
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(where)Tj
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2.8913 0 Td
(summer)Tj
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([)Tj
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(6)Tj
0 g
(,)Tj
0.83 0.64 0.02 0 k
(30)Tj
0 g
(,)Tj
0.83 0.64 0.02 0 k
(36)Tj
0 g
(].)Tj
3.8947 0 Td
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2.3981 0 Td
(light:dark)Tj
4.0195 0 Td
(synchronized)Tj
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5.5219 0 Td
[()]TJ
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(.)Tj
/F15 1 Tf
1.3096 0 Td
[()7()11()18()6()4(\n)4()]TJ
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4.0195 0 Td
(RCC299)Tj
3.5546 0 Td
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(over)Tj
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(a)Tj
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(of)Tj
1.0035 0 Td
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(subjected)Tj
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(to)Tj
1.0148 0 Td
(environ-)Tj
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(mentally-relevant)Tj
7.1375 0 Td
(HL)Tj
1.5137 0 Td
(or)Tj
1.0885 0 Td
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1.0148 0 Td
(HL+UV)Tj
3.5036 0 Td
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(cytometry,)Tj
4.439 0 Td
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(this)Tj
1.6498 0 Td
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2.4207 0 Td
(well)Tj
1.7972 0 Td
(with)Tj
1.9729 0 Td
(HL)Tj
1.5137 0 Td
(shifts,)Tj
2.5058 0 Td
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1 j
1 J
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7.4999 0 0 6.6659 537.8456 568.8566 cm
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1 TL
-0.0133 Tc
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(-2)Tj
ET
Q
q
1 j
1 J
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10 0 0 10 546.1228 564.3779 cm
BT
/F10 1 Tf
1 TL
-0.01 Tc
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Q
q
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7.4999 0 0 6.6659 549.6377 568.8566 cm
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1.3663 0 Td
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7.4999 0 0 6.6659 385.0015 529.8519 cm
BT
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1 TL
-0.0133 Tc
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(6)Tj
ET
Q
q
1 j
1 J
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1 TL
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(cells)Tj
1.8878 0 Td
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7.4999 0 0 6.6659 423.0992 529.8519 cm
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-0.0133 Tc
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(-1)Tj
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Q
q
1 j
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1.7631 0 Td
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1.4513 0 Td
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1 j
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7.4999 0 0 6.6659 485.2346 458.759 cm
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1 TL
-0.0133 Tc
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(0)Tj
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Q
q
1 j
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2.6192 0 Td
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1.6611 0 Td
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2.7154 0 Td
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1.1906 0 Td
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Q
q
1 j
1 J
0 w
7.4999 0 0 6.6659 522.5385 445.7196 cm
BT
/F10 1 Tf
1 TL
-0.0133 Tc
0 0 Td
(0)Tj
ET
Q
q
1 j
1 J
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-0.01 Tc
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(,)Tj
0.4422 0 Td
(quadrupli-)Tj
-33.046 -1.3039 Td
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1.9672 0 Td
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(35)Tj
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2.279 0 Td
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Q
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1 j
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7.4999 0 0 6.6659 365.2724 425.8204 cm
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-0.0133 Tc
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(-2)Tj
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Q
q
1 j
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(s)Tj
ET
Q
q
1 j
1 J
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7.4999 0 0 6.6659 377.0645 425.8204 cm
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-0.0133 Tc
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(-1)Tj
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Q
q
1 j
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7.4999 0 0 6.6659 219.9118 386.8724 cm
BT
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1 TL
-0.0133 Tc
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(-2)Tj
ET
Q
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1 j
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7.4999 0 0 6.6659 421.3417 386.8724 cm
BT
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(-2)Tj
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Q
q
1 j
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7.4999 0 0 6.6659 357.4488 341.7448 cm
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-0.0133 Tc
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(0)Tj
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Q
q
1 j
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7.4999 0 0 6.6659 399.2881 341.7448 cm
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-0.0133 Tc
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(2.5)Tj
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Q
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(\),)Tj
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(6)Tj
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7.4999 0 0 6.6659 439.37 341.7448 cm
BT
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1 TL
-0.0133 Tc
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(6)Tj
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Q
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1 j
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(9.5)Tj
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7.4999 0 0 6.6659 481.2094 341.7448 cm
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-0.0133 Tc
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(9.5)Tj
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Q
q
1 j
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7.4999 0 0 6.6659 549.9779 341.7448 cm
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1 TL
-0.0133 Tc
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(19.5)Tj
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Q
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1.4513 0 Td
(four)Tj
1.8878 0 Td
(biological)Tj
4.0309 0 Td
(replicates)Tj
3.9288 0 Td
(harvested)Tj
3.9855 0 Td
(at)Tj
0.9411 0 Td
(each)Tj
2.0012 0 Td
(time)Tj
2.0069 0 Td
(point,)Tj
2.5455 0 Td
(resulting)Tj
3.6794 0 Td
(in)Tj
1.0204 0 Td
(a)Tj
0.652 0 Td
(total)Tj
1.9729 0 Td
(of)Tj
1.0035 0 Td
(24)Tj
-36.527 -1.3039 Td
(samples)Tj
3.3391 0 Td
(\(biological)Tj
4.3654 0 Td
(triplicates)Tj
4.0592 0 Td
(from:)Tj
2.4037 0 Td
(Control)Tj
3.3165 0 Td
(T)Tj
ET
Q
q
1 j
1 J
0 w
7.4999 0 0 6.6659 380.9196 588.5291 cm
BT
/F10 1 Tf
1 TL
-0.0133 Tc
0 0 Td
(0)Tj
ET
Q
q
1 j
1 J
0 w
10 0 0 10 384.4346 590.1732 cm
BT
/F10 1 Tf
1 TL
-0.01 Tc
0 0 Td
(,)Tj
0.4365 0 Td
(T)Tj
ET
Q
q
1 j
1 J
0 w
7.4999 0 0 6.6659 394.8661 588.5291 cm
BT
/F10 1 Tf
1 TL
-0.0133 Tc
0 0 Td
(1)Tj
ET
Q
q
1 j
1 J
0 w
10 0 0 10 398.3811 590.1732 cm
BT
/F10 1 Tf
1 TL
-0.01 Tc
0 0 Td
(,)Tj
0.4365 0 Td
(T)Tj
ET
Q
q
1 j
1 J
0 w
7.4999 0 0 6.6659 408.8125 588.5291 cm
BT
/F10 1 Tf
1 TL
-0.0133 Tc
0 0 Td
(2.5)Tj
ET
Q
q
1 j
1 J
0 w
10 0 0 10 417.4299 590.1732 cm
BT
/F10 1 Tf
1 TL
-0.01 Tc
0 0 Td
(;)Tj
0.4422 0 Td
(HL)Tj
1.5136 0 Td
(T)Tj
ET
Q
q
1 j
1 J
0 w
7.4999 0 0 6.6659 442.9984 588.5291 cm
BT
/F10 1 Tf
1 TL
-0.0133 Tc
0 0 Td
(1)Tj
ET
Q
q
1 j
1 J
0 w
10 0 0 10 446.5133 590.1732 cm
BT
/F10 1 Tf
1 TL
-0.01 Tc
0 0 Td
(,)Tj
0.4422 0 Td
(T)Tj
ET
Q
q
1 j
1 J
0 w
7.4999 0 0 6.6659 456.9448 588.5291 cm
BT
/F10 1 Tf
1 TL
-0.0133 Tc
0 0 Td
(2.5)Tj
ET
Q
q
1 j
1 J
0 w
10 0 0 10 465.5622 590.1732 cm
BT
/F10 1 Tf
1 TL
-0.01 Tc
0 0 Td
(;)Tj
0.4422 0 Td
(HL+UV)Tj
3.5036 0 Td
(T)Tj
ET
Q
q
1 j
1 J
0 w
7.4999 0 0 6.6659 511.0866 588.5291 cm
BT
/F10 1 Tf
1 TL
-0.0133 Tc
0 0 Td
(1)Tj
ET
Q
q
1 j
1 J
0 w
10 0 0 10 514.6015 590.1732 cm
BT
/F10 1 Tf
1 TL
-0.01 Tc
0 0 Td
(,)Tj
0.4365 0 Td
(T)Tj
ET
Q
q
1 j
1 J
0 w
7.4999 0 0 6.6659 525.033 588.5291 cm
BT
/F10 1 Tf
1 TL
-0.0133 Tc
0 0 Td
(2.5)Tj
ET
Q
q
1 j
1 J
0 w
10 0 0 10 535.8614 590.1732 cm
BT
/F10 1 Tf
1 TL
-0.01 Tc
0 0 Td
(and)Tj
1.7121 0 Td
(an)Tj
-35.2967 -1.2982 Td
(additional)Tj
4.2179 0 Td
(set)Tj
1.2813 0 Td
(of)Tj
1.0034 0 Td
(T)Tj
ET
Q
q
1 j
1 J
0 w
7.4999 0 0 6.6659 271.1055 575.5464 cm
BT
/F10 1 Tf
1 TL
-0.0133 Tc
0 0 Td
(0)Tj
ET
Q
q
1 j
1 J
0 w
10 0 0 10 276.8314 577.1905 cm
BT
/F10 1 Tf
1 TL
-0.01 Tc
0 0 Td
(control)Tj
3.0784 0 Td
(samples)Tj
3.3391 0 Td
(from)Tj
2.1827 0 Td
(the)Tj
1.4513 0 Td
(HL+UV)Tj
3.5093 0 Td
(experiment\).)Tj
5.2667 0 Td
(Total)Tj
2.2904 0 Td
(RNA)Tj
2.2451 0 Td
(was)Tj
1.6781 0 Td
(extracted)Tj
-32.7229 -1.2982 Td
(with)Tj
1.9729 0 Td
(the)Tj
1.4513 0 Td
(RNeasy)Tj
3.2145 0 Td
(kit)Tj
1.2642 0 Td
(after)Tj
2.0069 0 Td
(homogenization)Tj
6.667 0 Td
(using)Tj
2.3584 0 Td
(the)Tj
1.4514 0 Td
(QIAshredder)Tj
5.4594 0 Td
(kit)Tj
1.2643 0 Td
(\(Qiagen,)Tj
3.6226 0 Td
(Germantown,)Tj
-30.7329 -1.2983 Td
(MD,)Tj
2.0579 0 Td
(USA\))Tj
2.4322 0 Td
(according)Tj
4.1327 0 Td
(to)Tj
1.0092 0 Td
(the)Tj
1.4513 0 Td
(manufacturer's)Tj
6.1852 0 Td
(instructions.)Tj
5.142 0 Td
(50)Tj
/F17 1 Tf
1.1622 0 Td
[()]TJ
/F10 1 Tf
(L)Tj
1.2529 0 Td
(of)Tj
1.0034 0 Td
(extracted)Tj
3.8325 0 Td
(RNA)Tj
2.245 0 Td
(was)Tj
1.6781 0 Td
(treated)Tj
-33.5846 -1.3039 Td
(with)Tj
1.9729 0 Td
(1)Tj
/F17 1 Tf
0.6917 0 Td
[()]TJ
/F10 1 Tf
(L)Tj
1.2529 0 Td
(of)Tj
0.9978 0 Td
(DNase)Tj
2.8855 0 Td
(\(TURBO)Tj
3.8154 0 Td
(DNA-)Tj
/F15 1 Tf
[( )-8()20()7()]TJ
/F17 1 Tf
[()]TJ
/F10 1 Tf
4.5411 0 Td
(Kit,)Tj
1.6611 0 Td
(Ambion,)Tj
3.736 0 Td
(Austin,)Tj
3.0898 0 Td
(TX,)Tj
1.6951 0 Td
(USA\))Tj
2.4321 0 Td
(at)Tj
0.9411 0 Td
(37C)Tj
2.1996 0 Td
(for)Tj
1.372 0 Td
(30)Tj
1.1565 0 Td
(min)Tj
-34.4406 -1.2983 Td
(according)Tj
4.1329 0 Td
(to)Tj
1.0148 0 Td
(the)Tj
1.4513 0 Td
(manufacturer's)Tj
6.1794 0 Td
(protocol.)Tj
3.7701 0 Td
(For)Tj
1.6044 0 Td
(further)Tj
2.9877 0 Td
(purification,)Tj
5.0853 0 Td
(a)Tj
0.6463 0 Td
(volume)Tj
3.1634 0 Td
(of)Tj
1.0035 0 Td
(4.8)Tj
1.3776 0 Td
(M)Tj
1.1055 0 Td
(LiCl)Tj
-33.5222 -1.2982 Td
(\(LiCl:sample)Tj
5.2271 0 Td
(1:1,)Tj
1.5987 0 Td
(v/v\))Tj
1.7744 0 Td
(was)Tj
1.6837 0 Td
(added,)Tj
2.8517 0 Td
(samples)Tj
3.3392 0 Td
(were)Tj
2.0976 0 Td
(placed)Tj
2.7552 0 Td
(at)Tj
0.9411 0 Td
(-20C)Tj
2.5455 0 Td
(for)Tj
1.372 0 Td
(4)Tj
0.686 0 Td
(to)Tj
1.0148 0 Td
(6)Tj
0.6916 0 Td
(h,)Tj
0.9581 0 Td
(and)Tj
1.7121 0 Td
(centrifuged)Tj
4.7225 0 Td
(at)Tj
-35.9713 -1.3039 Td
(16,100)Tj
2.7836 0 Td
(x)Tj
/F15 1 Tf
0.6803 0 Td
[(!)]TJ
/F10 1 Tf
0.6293 0 Td
(at)Tj
0.9411 0 Td
(4C)Tj
1.7291 0 Td
(for)Tj
1.3719 0 Td
(30)Tj
1.1565 0 Td
(min)Tj
1.8369 0 Td
(and)Tj
1.7121 0 Td
(then)Tj
1.9956 0 Td
(transferred)Tj
4.575 0 Td
(to)Tj
1.0148 0 Td
(fresh)Tj
2.16 0 Td
(tubes)Tj
2.3074 0 Td
(to)Tj
1.0148 0 Td
(which)Tj
2.6192 0 Td
(400)Tj
/F17 1 Tf
1.6271 0 Td
[()]TJ
/F10 1 Tf
(L)Tj
1.2529 0 Td
(70%)Tj
1.9105 0 Td
(ethanol)Tj
-33.3181 -1.2983 Td
(was)Tj
1.6781 0 Td
(added.)Tj
2.8516 0 Td
(After)Tj
2.2564 0 Td
(10)Tj
1.1564 0 Td
(min)Tj
1.8369 0 Td
(on)Tj
1.2642 0 Td
(ice,)Tj
1.5364 0 Td
(samples)Tj
3.3392 0 Td
(were)Tj
2.1033 0 Td
(spun)Tj
2.1486 0 Td
(at)Tj
0.9411 0 Td
(18,000)Tj
2.7893 0 Td
(x)Tj
/F15 1 Tf
0.6746 0 Td
[(!)]TJ
/F10 1 Tf
0.6293 0 Td
(for)Tj
1.3663 0 Td
(5)Tj
0.6917 0 Td
(min.)Tj
2.0579 0 Td
(The)Tj
1.7631 0 Td
(last)Tj
1.5364 0 Td
(two)Tj
1.6894 0 Td
(steps)Tj
-34.3102 -1.2983 Td
(were)Tj
2.0976 0 Td
(repeated,)Tj
3.8098 0 Td
(the)Tj
1.4513 0 Td
(supernatant)Tj
4.9151 0 Td
(removed)Tj
3.7077 0 Td
(and)Tj
1.7122 0 Td
(the)Tj
1.4513 0 Td
(pellet)Tj
2.3414 0 Td
(resuspended)Tj
5.1647 0 Td
(in)Tj
1.0261 0 Td
(TE)Tj
1.389 0 Td
(buffer.)Tj
2.8063 0 Td
(RNA)Tj
2.245 0 Td
(integrity)Tj
-34.1175 -1.3039 Td
(was)Tj
1.6781 0 Td
(determined)Tj
4.7905 0 Td
(using)Tj
2.364 0 Td
(a)Tj
0.6463 0 Td
(2100)Tj
2.0976 0 Td
(Bioanalyzer)Tj
4.8359 0 Td
(\(Agilent)Tj
3.4412 0 Td
(Technologies,)Tj
5.6806 0 Td
(Santa)Tj
2.3811 0 Td
(Clara,)Tj
2.5569 0 Td
(CA,)Tj
1.7744 0 Td
(USA\))Tj
2.4321 0 Td
(and)Tj
-34.6787 -1.2983 Td
(total)Tj
1.9729 0 Td
(RNA)Tj
2.245 0 Td
(was)Tj
1.6781 0 Td
(quantified)Tj
4.2519 0 Td
(on)Tj
1.2642 0 Td
(the)Tj
1.4513 0 Td
(Nano)Tj
2.4208 0 Td
(Drop)Tj
2.3301 0 Td
(system)Tj
2.897 0 Td
(\(Thermo)Tj
3.7814 0 Td
(Scientific,)Tj
4.0592 0 Td
(Waltham,)Tj
4.1272 0 Td
(MA,)Tj
2.0012 0 Td
(USA\).)Tj
-0.004 Tc
-33.2841 -1.2982 Td
(For)Tj
1.6271 0 Td
(short)Tj
2.2847 0 Td
(read)Tj
1.9786 0 Td
(sequencing,)Tj
4.9435 0 Td
(double)Tj
2.9537 0 Td
(stranded)Tj
3.7133 0 Td
(\(ds\))Tj
1.7915 0 Td
(cDNA)Tj
2.8006 0 Td
(was)Tj
1.6951 0 Td
(synthesized)Tj
4.8302 0 Td
(using)Tj
2.3868 0 Td
(the)Tj
1.4683 0 Td
(Ovation)Tj
-33.6696 -1.3039 Td
(RNA-seq)Tj
3.9005 0 Td
(System)Tj
3.0557 0 Td
(\(NuGEN)Tj
3.8436 0 Td
(Technologies)Tj
5.5332 0 Td
(Inc.,)Tj
1.9843 0 Td
(San)Tj
1.6781 0 Td
(Carlos,)Tj
3.0274 0 Td
(CA\))Tj
1.9048 0 Td
(according)Tj
4.1896 0 Td
(to)Tj
1.0261 0 Td
(manufacturer's)Tj
-30.1433 -1.2983 Td
(instructions)Tj
4.9946 0 Td
(except)Tj
2.7665 0 Td
(half)Tj
1.7065 0 Td
(the)Tj
1.4626 0 Td
(recommended)Tj
6.0321 0 Td
(amount)Tj
3.3506 0 Td
(of)Tj
1.0091 0 Td
(first-strand)Tj
4.6941 0 Td
(primer)Tj
2.9821 0 Td
(mix)Tj
1.7688 0 Td
(was)Tj
1.6894 0 Td
(used.)Tj
2.2847 0 Td
(Briefly,)Tj
-34.7411 -1.2983 Td
(RNA)Tj
2.262 0 Td
(was)Tj
1.6951 0 Td
(reverse-transcribed)Tj
7.9369 0 Td
(to)Tj
1.0261 0 Td
(generate)Tj
3.6057 0 Td
(first-strand)Tj
4.6941 0 Td
(cDNA)Tj
2.8006 0 Td
(using)Tj
2.3925 0 Td
(oligo-dT)Tj
3.702 0 Td
(and)Tj
1.7291 0 Td
(random)Tj
3.4299 0 Td
(hex-)Tj
-35.274 -1.2982 Td
(amer)Tj
2.2677 0 Td
(primers.)Tj
3.5773 0 Td
(Ds-cDNA)Tj
4.2462 0 Td
(was)Tj
1.7008 0 Td
(generated)Tj
4.1328 0 Td
(using)Tj
2.3925 0 Td
(DNA)Tj
2.3754 0 Td
(polymerase,)Tj
5.0059 0 Td
(and)Tj
1.7292 0 Td
(linearly)Tj
3.2088 0 Td
(amplified)Tj
4.0138 0 Td
(with)Tj
-34.6504 -1.3039 Td
(the)Tj
1.4627 0 Td
(Ribo-SPIA)Tj
4.524 0 Td
(method)Tj
3.3165 0 Td
([)Tj
0.83 0.64 0.02 0 k
(38)Tj
0 g
(].)Tj
2.0692 0 Td
(For)Tj
1.6158 0 Td
(all)Tj
1.1395 0 Td
(samples,)Tj
3.6 0 Td
(1)Tj
/F17 1 Tf
0.686 0 Td
[()]TJ
/F10 1 Tf
(g)Tj
1.1848 0 Td
(of)Tj
1.0092 0 Td
(the)Tj
1.4626 0 Td
(resulting)Tj
3.7191 0 Td
(ds-cDNA)Tj
4.0308 0 Td
(was)Tj
1.6894 0 Td
(used)Tj
2.0523 0 Td
(for)Tj
1.3833 0 Td
(library)Tj
-34.9452 -1.2983 Td
(preparation)Tj
4.9096 0 Td
(with)Tj
1.9956 0 Td
(half)Tj
1.7176 0 Td
(of)Tj
1.0148 0 Td
(the)Tj
1.4684 0 Td
(cDNA)Tj
2.8006 0 Td
(having)Tj
2.914 0 Td
(been)Tj
2.126 0 Td
(fragmented)Tj
4.8188 0 Td
(by)Tj
1.1792 0 Td
(sonication.)Tj
4.6091 0 Td
(The)Tj
1.7859 0 Td
(complete)Tj
3.8777 0 Td
(sam-)Tj
-35.2173 -1.2983 Td
(ple)Tj
1.406 0 Td
(\(fragmented)Tj
5.159 0 Td
(and)Tj
1.729 0 Td
(unfragmented)Tj
5.8961 0 Td
(cDNA\))Tj
3.1407 0 Td
(was)Tj
1.7008 0 Td
(electrophoresed)Tj
6.5707 0 Td
(on)Tj
1.2755 0 Td
(2.5%)Tj
2.1544 0 Td
(agarose)Tj
3.2144 0 Td
(gel)Tj
1.355 0 Td
(and)Tj
1.7348 0 Td
(size)Tj
-35.3364 -1.3039 Td
(selected)Tj
3.3449 0 Td
(for)Tj
1.3889 0 Td
(100200)Tj
3.5886 0 Td
(bp.)Tj
1.4683 0 Td
(After)Tj
2.2847 0 Td
(elution,)Tj
3.2655 0 Td
(cDNA)Tj
2.8006 0 Td
(fragments)Tj
4.2293 0 Td
(were)Tj
2.126 0 Td
(blunt-ended)Tj
5.1476 0 Td
(and)Tj
1.7292 0 Td
(ligated)Tj
2.88 0 Td
(to)Tj
1.0261 0 Td
(plat-)Tj
-35.2797 -1.2983 Td
(form)Tj
2.2053 0 Td
(specific)Tj
3.1918 0 Td
(ds-bar-coded)Tj
5.5275 0 Td
(adapters)Tj
3.5886 0 Td
(\(New)Tj
2.4038 0 Td
(England)Tj
3.5603 0 Td
(Biolabs,)Tj
3.3448 0 Td
(Ipswich,)Tj
3.566 0 Td
(MA\).)Tj
2.3641 0 Td
(Bar-coded)Tj
4.3653 0 Td
(sets)Tj
1.6668 0 Td
(of)Tj
-35.7843 -1.2982 Td
(12)Tj
1.1679 0 Td
(cDNA)Tj
2.8006 0 Td
(libraries)Tj
3.4696 0 Td
(were)Tj
2.1202 0 Td
(mixed)Tj
2.7269 0 Td
(in)Tj
1.0318 0 Td
(equal)Tj
2.3584 0 Td
(amounts)Tj
3.719 0 Td
(and)Tj
1.7292 0 Td
(sequenced)Tj
4.388 0 Td
(on)Tj
1.2755 0 Td
(the)Tj
1.4684 0 Td
(SOLiD)Tj
2.982 0 Td
(platform)Tj
-31.2375 -1.3039 Td
(\(Applied)Tj
3.7417 0 Td
(Biosystems,)Tj
4.8811 0 Td
(Foster)Tj
2.7043 0 Td
(City,)Tj
2.1316 0 Td
(CA\).)Tj
ET
Q
q
1 j
1 J
0 w
11.9999 0 0 11.9999 200.0125 256.0251 cm
BT
/F0 1 Tf
1 TL
-0.0033 Tc
0 0 Td
(Transcriptome)Tj
6.5433 0 Td
(analyses)Tj
ET
Q
q
1 j
1 J
0 w
10 0 0 10 200.0125 239.0173 cm
BT
/F10 1 Tf
1 TL
-0.004 Tc
0 0 Td
(Reads)Tj
2.5851 0 Td
(were)Tj
2.126 0 Td
(aligned)Tj
3.1294 0 Td
(to)Tj
1.0262 0 Td
(the)Tj
1.4683 0 Td
(RCC299)Tj
3.5943 0 Td
(nuclear)Tj
3.1975 0 Td
(genome)Tj
3.4072 0 Td
(using)Tj
2.3868 0 Td
(BWA)Tj
2.4491 0 Td
([)Tj
0.83 0.64 0.02 0 k
(39)Tj
0 g
(])Tj
1.8538 0 Td
(and)Tj
1.7291 0 Td
(to)Tj
1.0262 0 Td
(the)Tj
1.4683 0 Td
(plastid)Tj
2.8743 0 Td
(genome)Tj
-34.3216 -1.3039 Td
(using)Tj
2.3867 0 Td
(Bowtie)Tj
2.982 0 Td
([)Tj
0.83 0.64 0.02 0 k
(40)Tj
0 g
(].)Tj
2.075 0 Td
(The)Tj
1.7858 0 Td
(final)Tj
2.0012 0 Td
(mapped)Tj
3.4583 0 Td
(read)Tj
1.9786 0 Td
(numbers)Tj
3.7757 0 Td
(were)Tj
2.126 0 Td
(on)Tj
1.2755 0 Td
(average)Tj
3.2258 0 Td
(4.08)Tj
/F17 1 Tf
1.8709 0 Td
[()]TJ
/F10 1 Tf
0.788 0 Td
(0.97)Tj
1.8766 0 Td
(million)Tj
3.118 0 Td
(reads)Tj
-34.7241 -1.2982 Td
(per)Tj
1.5306 0 Td
(sample,)Tj
3.2485 0 Td
(with)Tj
1.9956 0 Td
(approximately)Tj
5.9754 0 Td
(half)Tj
1.7178 0 Td
(of)Tj
1.0148 0 Td
(these)Tj
2.2507 0 Td
(being)Tj
2.4321 0 Td
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