Additional file 3: Table S1. of Comparative transcriptome analysis of Gastrodia elata (Orchidaceae) in response to fungus symbiosis to identify gastrodin biosynthesis-related genes

Additional file 1: Figure S1. of Andrographis paniculata transcriptome provides molecular insights into tissue-specific accumulation of medicinal diterpenes

Anchal Garg (3525479)
Lalit Agrawal (1892533)
Rajesh Misra (3525482)
Shubha Sharma (3525476)
Sumit Ghosh (464456)

September 2015

Flow chart displaying strategies employed for de novo transcriptome analysis. Figure S2. Flow chart ...

Additional file 2: Table S2. of Comparative transcriptome analyses of flower development in four species of Achimenes (Gesneriaceae)

Wade Roberts (3291660)
Eric Roalson (3291663)

March 2017

Number of contigs detected as rRNAs and tRNAs in each transcriptome. (XLSX 33 kb

Additional file 2: Table S1. of Genome-wide analysis, molecular cloning and expression profiling reveal tissue-specifically expressed, feedback-regulated, stress-responsive and alternatively spliced novel genes involved in gibberellin metabolism in Salvia miltiorrhiza

Qing Du (1610224)
Caili Li (3554336)
Dongqiao Li (3554339)
Shanfa Lu (138566)

December 2015

Sequence features of gibberellin metabolism genes in A. thaliana. The accession numbers, cDNA length...

Additional file 5: Table S3. of Comparative transcriptome analysis of Gastrodia elata (Orchidaceae) in response to fungus symbiosis to identify gastrodin biosynthesis-related genes

Chi-Chu Tsai (668824)
Keh-Ming Wu (174958)
Tzen-Yuh Chiang (138945)
Chun-Yen Huang (3548543)
Chang-Hung Chou (504877)
Shu-Ju Li (3548540)
Yu-Chung Chiang (114878)

March 2016

Mapping of KEGG biological pathways for up-regulated (log2-FC ≥ 1, q-value < 0. 05, TMM-normalized F...

Additional file 2: Figure S2. of Comparative transcriptome analysis of Gastrodia elata (Orchidaceae) in response to fungus symbiosis to identify gastrodin biosynthesis-related genes

Chi-Chu Tsai (668824)
Keh-Ming Wu (174958)
Tzen-Yuh Chiang (138945)
Chun-Yen Huang (3548543)
Chang-Hung Chou (504877)
Shu-Ju Li (3548540)
Yu-Chung Chiang (114878)

March 2016

Unigenes identified solely or both for Armillaria mellea and juvenile tuber of Gastrodia elata in th...

Additional file 9: Table S6. of Comparative transcriptome analysis of Gastrodia elata (Orchidaceae) in response to fungus symbiosis to identify gastrodin biosynthesis-related genes

Chi-Chu Tsai (668824)
Keh-Ming Wu (174958)
Tzen-Yuh Chiang (138945)
Chun-Yen Huang (3548543)
Chang-Hung Chou (504877)
Shu-Ju Li (3548540)
Yu-Chung Chiang (114878)

March 2016

405 unigenes were significantly down-regulated (log2-FC ≤ -1, q-value < 0.05, TMM-normalized FPKM > ...

Additional file 10: Table S7. of Comparative transcriptome analysis of Gastrodia elata (Orchidaceae) in response to fungus symbiosis to identify gastrodin biosynthesis-related genes

Chi-Chu Tsai (668824)
Keh-Ming Wu (174958)
Tzen-Yuh Chiang (138945)
Chun-Yen Huang (3548543)
Chang-Hung Chou (504877)
Shu-Ju Li (3548540)
Yu-Chung Chiang (114878)

March 2016

Mapping of KEGG biological pathways for up-regulated (log2-FC ≥ 1, q-value < 0.05, TMM-normalized FP...

Additional file 1: Table S1. of Exploring the evolutionary origin of floral organs of Erycina pusilla, an emerging orchid model system

Anita Dirks-Mulder (3859090)
Roland Butôt (3593165)
Peter van Schaik (3859102)
Jan Wijnands (3859084)
Roel van den Berg (3859087)
Louie Krol (3859096)
Sadhana Doebar (3859105)
Kelly van Kooperen (3859108)
Hugo de Boer (745485)
Elena Kramer (3859099)
Erik Smets (206615)
Rutger Vos (3504797)
Alexander Vrijdaghs (3859093)
Barbara Gravendeel (579289)

March 2017

List of sequences used in the alignments and phylogenetic analyses. Table S2. Transcript primer sequ...

Additional file 1: of De novo transcriptome analysis of rose-scented geranium provides insights into the metabolic specificity of terpene and tartaric acid biosynthesis

Lokesh Narnoliya (3638002)
Girija Kaushal (3638005)
Sudhir Singh (619883)
Rajender Sangwan (174658)

January 2017

Figure S1. A phylogenetic tree generated on the basis of a plastid marker trnL-F in 57 Pelargonium s...

Additional file 1 of Transcriptomic analysis reveals candidate genes regulating development and host interactions of Colletotrichum fructicola

Xiaofei Liang (843086)
Shengping Shang (5568197)
Qiuyue Dong (3751315)
Bo Wang (86769)
Rong Zhang (44942)
Mark Gleason (3751306)
Guangyu Sun (429231)

July 2018

Table S1. Bioinformatic command lines used in this study. Table S2. qRT-PCR primers used in this stu...

Additional file 3: of Transcriptomic evidence for the control of soybean root isoflavonoid content by regulation of overlapping phenylpropanoid pathways

Mehran Dastmalchi (3631411)
Patrick Chapman (2548354)
Jaeju Yu (722728)
Ryan Austin (263006)
Sangeeta Dhaubhadel (766193)

January 2017

Figure S2. M-A plot of log2 fold change as a function of average expression of gene. Significantly d...

Additional file 3: of Gene regulatory networks on transfer entropy (GRNTE): a novel approach to reconstruct gene regulatory interactions applied to a case study for the plant pathogen Phytophthora infestans

Juan Castro (3448166)
Ivan Valdés (6566351)
Laura Gonzalez-García (6566354)
Giovanna Danies (662028)
Silvia Cañas (6566357)
Flavia Winck (6566360)
Carlos Ñústez (6566363)
Silvia Restrepo (204944)
Diego Riaño-Pachón (3430481)

April 2019

Table S2. Mean expression values for 48 TFs from P. infestans during the interaction with S. tuberos...

Additional file 3: Table S3. of Changes in the Sclerotinia sclerotiorum transcriptome during infection of Brassica napus

Shirin Seifbarghi (3877354)
M. Borhan (3484328)
Yangdou Wei (168452)
Cathy Coutu (455473)
Stephen Robinson (425911)
Dwayne Hegedus (455471)

March 2017

List of up-regulated genes with BLAST2GO annotation. Description of all genes that were up-regulated...

Additional file 2: of Gene co-expression network analysis reveals coordinated regulation of three characteristic secondary biosynthetic pathways in tea plant (Camellia sinensis)

Yuling Tai (3410630)
Chun Liu (47227)
Shuwei Yu (5636075)
Hua Yang (120668)
Jiameng Sun (5636078)
Chunxiao Guo (5518769)
Bei Huang (485021)
Zhaoye Liu (5636081)
Yi Yuan (180239)
Enhua Xia (5636084)
Chaoling Wei (408278)
Xiaochun Wan (408279)

August 2018

Modules significantly (pâ<â0.05) correlated with characteristic components in tea. (XLSX 11 kb

Additional file 3: of Transcriptome analysis reveals pathways facilitating the growth of tobacco powdery mildew in Arabidopsis

Ran Li (57928)
Ling-Li Zhang (482443)
Xue-Mei Yang (3216627)
Xiao-Long Cao (6202820)
Ying-Ge Wang (6202835)
Xian-Feng Ma (6306143)
Viswanathan Chandran (488420)
Jing Fan (149601)
Hui Yang (91136)
Jing Shang (227576)
Ji-Qun Zhao (6202838)
Shunyuan Xiao (722953)
Yan Li (23143)
Wen-Ming Wang (505701)

February 2019

Table S2. List of differentially expressed genes with more than 4-fold change between any two sample...

Additional file 1: Figure S1. of Andrographis paniculata transcriptome provides molecular insights into tissue-specific accumulation of medicinal diterpenes

Anchal Garg (3525479)
Lalit Agrawal (1892533)
Rajesh Misra (3525482)
Shubha Sharma (3525476)
Sumit Ghosh (464456)

September 2015

Flow chart displaying strategies employed for de novo transcriptome analysis. Figure S2. Flow chart ...

Additional file 2: Table S2. of Comparative transcriptome analyses of flower development in four species of Achimenes (Gesneriaceae)

Wade Roberts (3291660)
Eric Roalson (3291663)

March 2017

Number of contigs detected as rRNAs and tRNAs in each transcriptome. (XLSX 33 kb

Additional file 2: Table S1. of Genome-wide analysis, molecular cloning and expression profiling reveal tissue-specifically expressed, feedback-regulated, stress-responsive and alternatively spliced novel genes involved in gibberellin metabolism in Salvia miltiorrhiza

Qing Du (1610224)
Caili Li (3554336)
Dongqiao Li (3554339)
Shanfa Lu (138566)

December 2015

Sequence features of gibberellin metabolism genes in A. thaliana. The accession numbers, cDNA length...

Additional file 5: Table S3. of Comparative transcriptome analysis of Gastrodia elata (Orchidaceae) in response to fungus symbiosis to identify gastrodin biosynthesis-related genes

Chi-Chu Tsai (668824)
Keh-Ming Wu (174958)
Tzen-Yuh Chiang (138945)
Chun-Yen Huang (3548543)
Chang-Hung Chou (504877)
Shu-Ju Li (3548540)
Yu-Chung Chiang (114878)

March 2016

Mapping of KEGG biological pathways for up-regulated (log2-FC ≥ 1, q-value < 0. 05, TMM-normalized F...

Additional file 2: Figure S2. of Comparative transcriptome analysis of Gastrodia elata (Orchidaceae) in response to fungus symbiosis to identify gastrodin biosynthesis-related genes

Chi-Chu Tsai (668824)
Keh-Ming Wu (174958)
Tzen-Yuh Chiang (138945)
Chun-Yen Huang (3548543)
Chang-Hung Chou (504877)
Shu-Ju Li (3548540)
Yu-Chung Chiang (114878)

March 2016

Unigenes identified solely or both for Armillaria mellea and juvenile tuber of Gastrodia elata in th...

Additional file 9: Table S6. of Comparative transcriptome analysis of Gastrodia elata (Orchidaceae) in response to fungus symbiosis to identify gastrodin biosynthesis-related genes

Chi-Chu Tsai (668824)
Keh-Ming Wu (174958)
Tzen-Yuh Chiang (138945)
Chun-Yen Huang (3548543)
Chang-Hung Chou (504877)
Shu-Ju Li (3548540)
Yu-Chung Chiang (114878)

March 2016

405 unigenes were significantly down-regulated (log2-FC ≤ -1, q-value < 0.05, TMM-normalized FPKM > ...

Additional file 10: Table S7. of Comparative transcriptome analysis of Gastrodia elata (Orchidaceae) in response to fungus symbiosis to identify gastrodin biosynthesis-related genes

Chi-Chu Tsai (668824)
Keh-Ming Wu (174958)
Tzen-Yuh Chiang (138945)
Chun-Yen Huang (3548543)
Chang-Hung Chou (504877)
Shu-Ju Li (3548540)
Yu-Chung Chiang (114878)

March 2016

Mapping of KEGG biological pathways for up-regulated (log2-FC ≥ 1, q-value < 0.05, TMM-normalized FP...

Additional file 1: Table S1. of Exploring the evolutionary origin of floral organs of Erycina pusilla, an emerging orchid model system

Anita Dirks-Mulder (3859090)
Roland Butôt (3593165)
Peter van Schaik (3859102)
Jan Wijnands (3859084)
Roel van den Berg (3859087)
Louie Krol (3859096)
Sadhana Doebar (3859105)
Kelly van Kooperen (3859108)
Hugo de Boer (745485)
Elena Kramer (3859099)
Erik Smets (206615)
Rutger Vos (3504797)
Alexander Vrijdaghs (3859093)
Barbara Gravendeel (579289)

March 2017

List of sequences used in the alignments and phylogenetic analyses. Table S2. Transcript primer sequ...

Additional file 1: of De novo transcriptome analysis of rose-scented geranium provides insights into the metabolic specificity of terpene and tartaric acid biosynthesis

Lokesh Narnoliya (3638002)
Girija Kaushal (3638005)
Sudhir Singh (619883)
Rajender Sangwan (174658)

January 2017

Figure S1. A phylogenetic tree generated on the basis of a plastid marker trnL-F in 57 Pelargonium s...

Additional file 1 of Transcriptomic analysis reveals candidate genes regulating development and host interactions of Colletotrichum fructicola

Xiaofei Liang (843086)
Shengping Shang (5568197)
Qiuyue Dong (3751315)
Bo Wang (86769)
Rong Zhang (44942)
Mark Gleason (3751306)
Guangyu Sun (429231)

July 2018

Table S1. Bioinformatic command lines used in this study. Table S2. qRT-PCR primers used in this stu...

Additional file 3: of Transcriptomic evidence for the control of soybean root isoflavonoid content by regulation of overlapping phenylpropanoid pathways

Mehran Dastmalchi (3631411)
Patrick Chapman (2548354)
Jaeju Yu (722728)
Ryan Austin (263006)
Sangeeta Dhaubhadel (766193)

January 2017

Figure S2. M-A plot of log2 fold change as a function of average expression of gene. Significantly d...

Additional file 3: of Gene regulatory networks on transfer entropy (GRNTE): a novel approach to reconstruct gene regulatory interactions applied to a case study for the plant pathogen Phytophthora infestans

Juan Castro (3448166)
Ivan Valdés (6566351)
Laura Gonzalez-García (6566354)
Giovanna Danies (662028)
Silvia Cañas (6566357)
Flavia Winck (6566360)
Carlos Ñústez (6566363)
Silvia Restrepo (204944)
Diego Riaño-Pachón (3430481)

April 2019

Table S2. Mean expression values for 48 TFs from P. infestans during the interaction with S. tuberos...

Additional file 3: Table S3. of Changes in the Sclerotinia sclerotiorum transcriptome during infection of Brassica napus

Shirin Seifbarghi (3877354)
M. Borhan (3484328)
Yangdou Wei (168452)
Cathy Coutu (455473)
Stephen Robinson (425911)
Dwayne Hegedus (455471)

March 2017

List of up-regulated genes with BLAST2GO annotation. Description of all genes that were up-regulated...

Additional file 2: of Gene co-expression network analysis reveals coordinated regulation of three characteristic secondary biosynthetic pathways in tea plant (Camellia sinensis)

Yuling Tai (3410630)
Chun Liu (47227)
Shuwei Yu (5636075)
Hua Yang (120668)
Jiameng Sun (5636078)
Chunxiao Guo (5518769)
Bei Huang (485021)
Zhaoye Liu (5636081)
Yi Yuan (180239)
Enhua Xia (5636084)
Chaoling Wei (408278)
Xiaochun Wan (408279)

August 2018

Modules significantly (pâ<â0.05) correlated with characteristic components in tea. (XLSX 11 kb

Additional file 3: of Transcriptome analysis reveals pathways facilitating the growth of tobacco powdery mildew in Arabidopsis

Ran Li (57928)
Ling-Li Zhang (482443)
Xue-Mei Yang (3216627)
Xiao-Long Cao (6202820)
Ying-Ge Wang (6202835)
Xian-Feng Ma (6306143)
Viswanathan Chandran (488420)
Jing Fan (149601)
Hui Yang (91136)
Jing Shang (227576)
Ji-Qun Zhao (6202838)
Shunyuan Xiao (722953)
Yan Li (23143)
Wen-Ming Wang (505701)

February 2019

Table S2. List of differentially expressed genes with more than 4-fold change between any two sample...

Additional file 1: Figure S1. of Andrographis paniculata transcriptome provides molecular insights into tissue-specific accumulation of medicinal diterpenes

Anchal Garg (3525479)
Lalit Agrawal (1892533)
Rajesh Misra (3525482)
Shubha Sharma (3525476)
Sumit Ghosh (464456)

September 2015

Flow chart displaying strategies employed for de novo transcriptome analysis. Figure S2. Flow chart ...

Additional file 2: Table S2. of Comparative transcriptome analyses of flower development in four species of Achimenes (Gesneriaceae)

Wade Roberts (3291660)
Eric Roalson (3291663)

March 2017

Number of contigs detected as rRNAs and tRNAs in each transcriptome. (XLSX 33 kb

Additional file 2: Table S1. of Genome-wide analysis, molecular cloning and expression profiling reveal tissue-specifically expressed, feedback-regulated, stress-responsive and alternatively spliced novel genes involved in gibberellin metabolism in Salvia miltiorrhiza

Qing Du (1610224)
Caili Li (3554336)
Dongqiao Li (3554339)
Shanfa Lu (138566)

December 2015

Sequence features of gibberellin metabolism genes in A. thaliana. The accession numbers, cDNA length...

Additional file 3: Table S1. of Comparative transcriptome analysis of Gastrodia elata (Orchidaceae) in response to fungus symbiosis to identify gastrodin biosynthesis-related genes

Abstract

Extracted data

Additional file 3: Table S1. of Comparative transcriptome analysis of Gastrodia elata (Orchidaceae) in response to fungus symbiosis to identify gastrodin biosynthesis-related genes

Abstract

Extracted data

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