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Xiaojing Zhang, Xuyang Liu, Dengfeng Zhang, Huaijun Tang, Baocheng Sun, Chunhui Li, Luyang Hao, Cheng Liu, Yongxiang Li, Yunsu Shi, Xiaoqing Xie, Yanchun Song, Tianyu Wang, Yu Li
Genome-wide identification of gene expression in contrasting maize inbred lines under field drought conditions reveals the significance of transcription factors in drought tolerance
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(mington,)Tj
3.9004 0 Td
(DE\))Tj
1.8652 0 Td
(and)Tj
1.7291 0 Td
(Bioanalyzer)Tj
4.8982 0 Td
(2100)Tj
2.126 0 Td
(using)Tj
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(RNA)Tj
2.262 0 Td
(Nano)Tj
2.4435 0 Td
(6000)Tj
2.1259 0 Td
(Assay)Tj
2.5115 0 Td
(Kit)Tj
1.4627 0 Td
(\(Agilent)Tj
3.4922 0 Td
(Technologies,)Tj
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(CA,)Tj
1.7914 0 Td
(USA\).)Tj
2.6816 0 Td
(The)Tj
1.7801 0 Td
(RNA)Tj
2.2621 0 Td
(concentration)Tj
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(Qubit)Tj
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(RNA)Tj
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(Assay)Tj
2.5171 0 Td
(Kit)Tj
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(in)Tj
1.0375 0 Td
(Qubit)Tj
2.5682 0 Td
(2.0)Tj
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2.075 0 Td
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(CA,)Tj
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(USA\).)Tj
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(Ultra)Tj
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(RNA)Tj
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(Kit)Tj
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(Illumina)Tj
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(\(NEB,)Tj
2.6702 0 Td
(MA,)Tj
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(USA\).)Tj
2.6816 0 Td
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3.0784 0 Td
(mRNA)Tj
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1.6951 0 Td
(attached)Tj
3.5886 0 Td
(to)Tj
1.0261 0 Td
(magnetic)Tj
3.9005 0 Td
(beads)Tj
2.4718 0 Td
(with)Tj
1.9956 0 Td
(oligo\(dT\),)Tj
4.2576 0 Td
(and)Tj
1.7291 0 Td
(then)Tj
2.0182 0 Td
(cleaved)Tj
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(short)Tj
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(fragments)Tj
4.2293 0 Td
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-34.1969 -1.2982 Td
(divalent)Tj
3.4185 0 Td
(cations)Tj
3.0614 0 Td
(under)Tj
2.6192 0 Td
(elevated)Tj
3.4469 0 Td
(temperature.)Tj
5.3575 0 Td
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2.33 0 Td
(the)Tj
1.4684 0 Td
(first)Tj
1.8085 0 Td
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(of)Tj
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(random)Tj
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(hexamer)Tj
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3.5773 0 Td
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5.743 0 Td
(second)Tj
3.016 0 Td
(strand)Tj
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(cDNA)Tj
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(synthesis)Tj
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(was)Tj
1.6951 0 Td
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-32.9156 -1.3039 Td
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(DNA)Tj
2.3754 0 Td
(polymerase)Tj
4.7792 0 Td
(I)Tj
0.5613 0 Td
(and)Tj
1.7291 0 Td
(RNase)Tj
2.8006 0 Td
(H,)Tj
1.2076 0 Td
(and)Tj
1.7347 0 Td
(then)Tj
2.0183 0 Td
(cDNA)Tj
2.8006 0 Td
(was)Tj
1.6951 0 Td
(ligated)Tj
2.8857 0 Td
(with)Tj
1.9955 0 Td
(adaptors.)Tj
3.8948 0 Td
(These)Tj
2.5682 0 Td
(frag-)Tj
-35.4328 -1.2983 Td
(ments)Tj
2.6702 0 Td
(were)Tj
2.1203 0 Td
(purified)Tj
3.4129 0 Td
(and)Tj
1.7291 0 Td
(used)Tj
2.0579 0 Td
(as)Tj
1.0148 0 Td
(templates)Tj
4.0422 0 Td
(for)Tj
1.389 0 Td
(PCR)Tj
2.0636 0 Td
(amplification)Tj
5.5388 0 Td
(to)Tj
1.0205 0 Td
(construct)Tj
3.9798 0 Td
(the)Tj
1.474 0 Td
(sequencing)Tj
-32.5131 -1.2983 Td
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2.8006 0 Td
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Q
q
1 j
1 J
0 w
11.9999 0 0 11.9999 200.0125 550.9417 cm
BT
/F0 1 Tf
1 TL
-0.0033 Tc
0 0 Td
(Sequencing)Tj
5.4331 0 Td
(data)Tj
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Q
q
1 j
1 J
0 w
10 0 0 10 200.0125 533.9338 cm
BT
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1 TL
-0.017 Tc
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1.7404 0 Td
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1.6724 0 Td
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3.9402 0 Td
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1.7518 0 Td
(USA\).)Tj
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4.3993 0 Td
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(\(e.g.)Tj
1.8369 0 Td
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(poly-N,)Tj
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(than)Tj
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(10%)Tj
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(base,)Tj
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(or)Tj
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1.9445 0 Td
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2.9197 0 Td
(than)Tj
1.9729 0 Td
(50%)Tj
1.8935 0 Td
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2.2394 0 Td
(whose)Tj
2.6589 0 Td
(Q)Tj
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Q
q
1 j
1 J
0 w
7.4999 0 0 6.6659 415.2755 506.2677 cm
BT
/F5 1 Tf
1 TL
-0.0226 Tc
0 0 Td
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ET
Q
q
1 j
1 J
0 w
10 0 0 10 434.5511 507.9118 cm
BT
/F5 1 Tf
1 TL
-0.017 Tc
0 0 Td
(lower)Tj
2.3867 0 Td
(than)Tj
1.9786 0 Td
(20\))Tj
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(clean)Tj
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(maize)Tj
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(B73_RefGen_v3)Tj
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1.6895 0 Td
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(files)Tj
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0.83 0.64 0.02 0 k
2.1543 0 Td
(ftp://ftp.ensemblgenomes.org)Tj
11.4007 0 Td
(/pub/plants/)Tj
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(release-24/fasta/zea_mays/)Tj
0 g
10.5052 0 Td
(and)Tj
0.83 0.64 0.02 0 k
1.6951 0 Td
(ftp://ftp.ensemblgenomes.org/pub/plan)Tj
15.2388 0 Td
(ts/release-24/gtf/zea_)Tj
-27.4391 -1.2983 Td
(mays/)Tj
0 g
(.)Tj
2.7666 0 Td
(Tophat2)Tj
3.498 0 Td
([)Tj
0.83 0.64 0.02 0 k
(44)Tj
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(])Tj
1.8028 0 Td
(software)Tj
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(align)Tj
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(clean)Tj
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(reads)Tj
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(to)Tj
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(the)Tj
1.4286 0 Td
(reference)Tj
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(genome)Tj
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(reads)Tj
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3.787 0 Td
([)Tj
0.83 0.64 0.02 0 k
(45)Tj
0 g
(].)Tj
2.0125 0 Td
(Cuffdiff)Tj
3.2542 0 Td
(was)Tj
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(to)Tj
0.9978 0 Td
(calculate)Tj
-32.9667 -1.2983 Td
(the)Tj
1.4287 0 Td
(FPKM)Tj
2.8233 0 Td
(\(fragments)Tj
4.439 0 Td
(per)Tj
1.491 0 Td
(kilo)Tj
1.6838 0 Td
(base)Tj
1.8935 0 Td
(of)Tj
0.9921 0 Td
(transcript)Tj
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(per)Tj
1.491 0 Td
(million)Tj
3.033 0 Td
(fragments)Tj
4.1158 0 Td
(mapped\))Tj
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(of)Tj
0.9864 0 Td
(each)Tj
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(gene.)Tj
-34.0438 -1.3039 Td
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(clustering)Tj
4.0252 0 Td
(analysis)Tj
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0.9922 0 Td
(samples)Tj
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(transcripomes)Tj
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(the)Tj
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Q
q
1 j
1 J
0 w
7.4999 0 0 6.6659 532.5165 415.2755 cm
BT
/F5 1 Tf
1 TL
-0.0226 Tc
0 0 Td
(2)Tj
ET
Q
q
1 j
1 J
0 w
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BT
/F5 1 Tf
1 TL
-0.017 Tc
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(\(FPKM)Tj
-33.5903 -1.2982 Td
(+)Tj
0.788 0 Td
(1\))Tj
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(PCA)Tj
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(analysis)Tj
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(sampels')Tj
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1.6894 0 Td
(plotted)Tj
2.9481 0 Td
(by)Tj
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(DESeq)Tj
2.8686 0 Td
([)Tj
0.83 0.64 0.02 0 k
(46)Tj
0 g
(])Tj
1.7972 0 Td
(package)Tj
3.3222 0 Td
(in)Tj
1.0091 0 Td
(R)Tj
0.8277 0 Td
(software.)Tj
ET
Q
q
1 j
1 J
0 w
11.9999 0 0 11.9999 200.0125 364.4787 cm
BT
/F0 1 Tf
1 TL
-0.0033 Tc
0 0 Td
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4.937 0 Td
(expression)Tj
4.9937 0 Td
(analysis)Tj
ET
Q
q
1 j
1 J
0 w
10 0 0 10 200.0125 347.4708 cm
BT
/F5 1 Tf
1 TL
-0.004 Tc
0 0 Td
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1.3379 0 Td
(identify)Tj
3.2938 0 Td
(genes)Tj
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(with)Tj
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(levels,)Tj
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(a)Tj
0.6577 0 Td
(pairwise)Tj
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(comparison)Tj
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-34.1402 -1.2982 Td
([)Tj
0.83 0.64 0.02 0 k
(46)Tj
0 g
(])Tj
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(was)Tj
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2.2847 0 Td
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3.0784 0 Td
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1.3833 0 Td
(each)Tj
2.0296 0 Td
(library,)Tj
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(the)Tj
1.474 0 Td
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3.9685 0 Td
(Alignment/Map)Tj
6.6954 0 Td
(\(SAM\))Tj
2.9537 0 Td
(files)Tj
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(created)Tj
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(were)Tj
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1.0261 0 Td
(calculate)Tj
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(mapped)Tj
3.4639 0 Td
(reads)Tj
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(of)Tj
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(the)Tj
1.4683 0 Td
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(by)Tj
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(HTSeq)Tj
3.0048 0 Td
([)Tj
0.83 0.64 0.02 0 k
(47)Tj
0 g
(].)Tj
2.0806 0 Td
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2.33 0 Td
(the)Tj
1.4684 0 Td
(read)Tj
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(normalization)Tj
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1.1735 0 Td
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(based)Tj
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(the)Tj
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(negative)Tj
3.5263 0 Td
(binomial)Tj
-33.9985 -1.2983 Td
(distribution)Tj
4.9662 0 Td
(model.)Tj
2.9707 0 Td
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1.1055 0 Td
(addition,)Tj
3.8268 0 Td
(the)Tj
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1.4683 0 Td
[()]TJ
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0.771 0 Td
(value)Tj
2.3017 0 Td
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1.0148 0 Td
(the)Tj
1.474 0 Td
(results)Tj
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1.7008 0 Td
(adjusted)Tj
3.5773 0 Td
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2.3868 0 Td
(the)Tj
1.4683 0 Td
(Benjamini)Tj
-31.8385 -1.3039 Td
(and)Tj
1.7291 0 Td
(Hochberg's)Tj
4.7905 0 Td
(approach)Tj
3.9515 0 Td
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1.0261 0 Td
(control)Tj
3.1181 0 Td
(the)Tj
1.4683 0 Td
(false)Tj
1.9729 0 Td
(discovery)Tj
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1.7461 0 Td
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2.0239 0 Td
(comparison)Tj
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(assays)Tj
-33.8284 -1.2982 Td
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3.9911 0 Td
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1.7802 0 Td
(first)Tj
1.8084 0 Td
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(expression)Tj
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3.4469 0 Td
(and)Tj
1.7291 0 Td
(well-watered)Tj
-30.5459 -1.2983 Td
(environments)Tj
5.7883 0 Td
(of)Tj
1.0148 0 Td
(the)Tj
1.474 0 Td
(same)Tj
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(genotype)Tj
3.8551 0 Td
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1.0262 0 Td
(detect)Tj
2.6192 0 Td
(drought)Tj
3.4412 0 Td
(responsive)Tj
4.456 0 Td
(genes,)Tj
2.6646 0 Td
(including)Tj
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(four)Tj
1.9162 0 Td
(com-)Tj
-34.5541 -1.3039 Td
(parison)Tj
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(groups:)Tj
3.1917 0 Td
(HMD-HMC,)Tj
5.5162 0 Td
(LMD-LMC,)Tj
5.057 0 Td
(HSD-HSC)Tj
4.456 0 Td
(and)Tj
1.7348 0 Td
(LSD-LSC.)Tj
4.2236 0 Td
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1.7802 0 Td
(second)Tj
3.0104 0 Td
(assay)Tj
2.2677 0 Td
(com-)Tj
-34.4634 -1.2983 Td
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2.4944 0 Td
(genes)Tj
2.4378 0 Td
(expression)Tj
4.4674 0 Td
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1.0148 0 Td
(the)Tj
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(different)Tj
3.6567 0 Td
(genotypes)Tj
4.2179 0 Td
(under)Tj
2.6192 0 Td
(the)Tj
1.474 0 Td
(same)Tj
2.2564 0 Td
(environment)Tj
5.4311 0 Td
(to)Tj
1.0262 0 Td
(detect)Tj
-32.5642 -1.2983 Td
(genotypic)Tj
4.1215 0 Td
(differentially)Tj
5.3064 0 Td
(expressed)Tj
4.0932 0 Td
(genes,)Tj
2.6702 0 Td
(including)Tj
4.0422 0 Td
(four)Tj
1.9106 0 Td
(comparison)Tj
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(groups:)Tj
3.1918 0 Td
(HMD-LMD,)Tj
-30.3135 -1.2982 Td
(HMC-LMC,)Tj
5.21 0 Td
(HSD-LSD)Tj
4.303 0 Td
(and)Tj
1.7291 0 Td
(HSC-LSC.)Tj
ET
Q
q
1 j
1 J
0 w
11.9999 0 0 11.9999 200.0125 178.0157 cm
BT
/F0 1 Tf
1 TL
-0.0033 Tc
0 0 Td
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2.6409 0 Td
(function)Tj
3.6804 0 Td
(annotation)Tj
4.8283 0 Td
(analysis)Tj
ET
Q
q
1 j
1 J
0 w
10 0 0 10 200.0125 161.0078 cm
BT
/F5 1 Tf
1 TL
-0.004 Tc
0 0 Td
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2.33 0 Td
(Ontology)Tj
3.9912 0 Td
(analysis)Tj
3.3278 0 Td
(was)Tj
1.7008 0 Td
(conducted)Tj
4.4277 0 Td
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