Wavelet packets are a powerful, flexible and computationally cheap form of adapted ... many new applications in signal processing in domains such as image, ... frequency tiling of the signal (best basis), the adapted WP decomposition is far ...
Sep 23, 2005 - was supported by the DOD STTR and the DARPA. University Photonics Research Program. *Electronic address: [email protected].
Williamsburg, VA and in the Technical Report [8]. This work was ...... all the eigenvalues ofAindeed changes roughly quadratically inn, in contrast to the classical ...
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Email [jemanuel,wysotzki]@cs.tu-berlin.de. Abstract. ..... HTML which is used for displaying documents in the web). Tag based ... ing stylesheets (CSS). XSL (Extensible ... mation can involve recursive template applications. (Note that some of ...
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Dec 8, 2016 - Jonathan M. Scholey 1,*, Gul Civelekoglu-Scholey 1 and Ingrid ...... Pidoux, A.L.; Uzawa, S.; Perry, P.E.; Cande, W.Z.; Allshire, R.C. Live ...
Asian Pacific Journal of Cancer Prevention, Vol 5, 2004. 433 α-Mangostin Inhibition of Preneoplastic Lesions in the Colon. Asian Pacific J Cancer Prev, 5, 433- ...
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1Department of Computer Networks, Ahram Canadian University, 6th October City,. Egypt ... cryptographic operations; permutation, and substitution. Round key ...
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Aug 24, 2017 - David J. Moore1 ... Citation: Moore RC, Paolillo EW, Heaton A, Fazeli ..... fied version of the Lawton and Brody scale (Heaton et al., 2004).
II: Tophat alignment summary Mock Left reads: Input: 155260083 Mapped: 151390295 (97.5% of input) of these: 20789836 (13.7%) have multiple alignments (331 have >20) Right reads: Input: 155260083 Mapped: 151356721 (97.5% of input) of these: 20778336 (13.7%) have multiple alignments (373 have >20) 97.5% overall read alignment rate.
Aligned pairs: 149669813 of these: 17502335 (11.7%) have multiple alignments and:
158470 ( 0.1%) are discordant alignments
96.3% concordant pair alignment rate.
5
TCV Left reads: Input: 170379319 Mapped: 152532447 (89.5% of input) of these: 10760144 ( 7.1%) have multiple alignments (440 have >20) Right reads: Input: 170379319 Mapped: 152453823 (89.5% of input) of these: 10752126 ( 7.1%) have multiple alignments (460 have >20) 89.5% overall read alignment rate.
Aligned pairs: 150493084 of these: 7517350 ( 5.0%) have multiple alignments and:
302293 ( 0.2%) are discordant alignments
88.2% concordant pair alignment rate.
6
III: Methods and parameters for analysing RNA-Seq data using tophat and cufflinks: 1. Map the reads for each sample to the reference genome tophat -p 8 -G all.gff3 -r 60 -o 1th R1_001.fastq R2_001.fastq 2. Assemble transcripts for each sample with reference gene structure cufflinks -g ../all.gff3 -p 8 -o mock_cl mock_tophat/accepted_hits.bam cufflinks -g ../all.gff3 -p 8 -o TCV_cl TCV_tophat/accepted_hits.bam 3. Run Cuffcompare on all assemblies to create a single merged transcriptome annotation: cuffcompare -o TCV -s At.fa -r ../all.gff3 -R -C mock_cl/transcripts.gtf TCV_cl/transcripts.gtf 4. Run Cuffdiff by using the merged transcriptome assembly along with the BAM from Tophat for each replicate cuffdiff -o diff1 -b Mt.fa -p 8 –L mock,TCV -u 1_cuffcompare/\1.combined.gtf \./mock_tophat/accepted_hits.bam \./TCV_tophat/accepted_hits.bam
7
Genome-wide transcriptomic analysis reveals correlation between higher WRKY61 expression and reduced symptom severity in Turnip crinkle virus infected Arabidopsis thaliana Ruimin Gao, Peng Liu, Yuhan Yong, and Sek-Man Wong
Supplementary Table S4 Comparison of RNA-seq data and qRT-PCR Gene ID
Gene symbol
AT2G19900
ATNADPME1
AT3G28510
Tri Hyd
AT1G66700
PXMT1
AT1G52690
LEA7
AT2G29470
ATGSTU3
AT2G26020 AT5G44430 AT3G16670
PDF1.2B PDF1.2C Ole e 1
AT5G20630
GLP3
AT2G10940
F15K19.1
AT3G22380 AT3G61220
TIC SDR1
AT5G52240
MSBP1
AT5G53300
UBC10
AT3G18820
ATRABG3F
Gene name
Fold change qRT-PCR (CBP20)
NADP-malic enzyme 1 [Source:TAIR_LOCUS;Acc: AT2G19900] P-loop containing nucleoside triphosphate hydrolases superfamily protein; S-adenosyl-L-methioninedependent methyltransferases superfamily protein Late embryogenesis abundant protein (LEA) family protein glutathione S-transferase tau 3 plant defensin 1.2b plant defensin 1.2C Pollen Ole e 1 allergen and extensin family protein germin 3. Encodes a germinlike protein Bifunctional inhibitor/lipidtransfer protein/seed storage 2S albumin superfamily protein time for coffee NAD(P)-binding Rossmannfold superfamily protein membrane steroid binding protein 1 ubiquitin-conjugating enzyme 10 Ras small GTPase, Rab type
1
RNASeq
8.97
qRTPCR (Tubu lin) 9.87
8.85
9.72
10.55
2.73
3.67
9.17
9.30
10.16
9.10
6.62
7.48
8.66
-10.52 -7.99 -9.37
-9.67 -7.12 -8.51
-10.84 -10.70 -10.21
-9.03
-8.21
-9.26
-8.08
-7.24
-8.37
-0.10 -0.11
0.77 0.74
0.01 0.00
0.42
1.30
0.00
0.16
1.09
0.00
-0.06
0.80
-0.01
11.92
Genome-wide transcriptomic analysis reveals correlation between higher WRKY61 expression and reduced symptom severity in Turnip crinkle virus infected Arabidopsis thaliana Ruimin Gao, Peng Liu, Yuhan Yong, and Sek-Man Wong
Supplementary Table S5 Primers used in this study Primers
