Additional file 10: of Comparative transcriptomics identifies patterns of selection in roses

Additional file 1: of Comparative genomics and transcriptomics analysis reveals evolution patterns of selection in the Salix phylogeny

You-jie Zhao (5816699)
Xin-yi Liu (6529286)
Ran Guo (1633090)
Kun-rong Hu (6529289)
Yong Cao (9208)
Fei Dai (211873)

March 2019

Table S1. Main geographic distributions of 9 Salix used in this work. Table S2. Geographic distribut...

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 8: Table S3. of Transcriptome-wide functional characterization reveals novel relationships among differentially expressed transcripts in developing soybean embryos

Delasa Aghamirzaie (3550586)
Dhruv Batra (3580100)
Lenwood Heath (3580097)
Andrew Schneider (3580094)
Ruth Grene (18292)
Eva Collakova (3550583)

November 2015

Summary of all information relevant to 2,938 transcripts. This file contains the following informati...

Additional file 8: of Comparative transcriptomics identifies patterns of selection in roses

Shubin Li (756060)
Micai Zhong (6114584)
Xue Dong (545412)
Xiaodong Jiang (456292)
Yuxing Xu (2988792)
Yibo Sun (6114593)
Fang Cheng (138729)
De-zhu Li (5875247)
Kaixue Tang (6114599)
Siqing Wang (5572508)
Silan Dai (620222)
Jin-Yong Hu (3451760)

December 2018

Table S6. Raw data for the positively selected genes in the Rosaceae-common transcripts. (XLSX 185 k...

Additional file 2: of Comparative transcriptomics identifies patterns of selection in roses

Shubin Li (756060)
Micai Zhong (6114584)
Xue Dong (545412)
Xiaodong Jiang (456292)
Yuxing Xu (2988792)
Yibo Sun (6114593)
Fang Cheng (138729)
De-zhu Li (5875247)
Kaixue Tang (6114599)
Siqing Wang (5572508)
Silan Dai (620222)
Jin-Yong Hu (3451760)

December 2018

Table S2. Annotation details for both genotypes. COG, GO, KEGG, KOG, Pfam, Swissprot, TrEMBL, NR and...

Additional file 5: of Comparative transcriptomics identifies patterns of selection in roses

Shubin Li (756060)
Micai Zhong (6114584)
Xue Dong (545412)
Xiaodong Jiang (456292)
Yuxing Xu (2988792)
Yibo Sun (6114593)
Fang Cheng (138729)
De-zhu Li (5875247)
Kaixue Tang (6114599)
Siqing Wang (5572508)
Silan Dai (620222)
Jin-Yong Hu (3451760)

December 2018

Table S4. KEGG and GO clustering information of 4447 Rosaceae-common genes. (XLSX 274 kb

Additional file 11: of Comparative transcriptomics identifies patterns of selection in roses

Shubin Li (756060)
Micai Zhong (6114584)
Xue Dong (545412)
Xiaodong Jiang (456292)
Yuxing Xu (2988792)
Yibo Sun (6114593)
Fang Cheng (138729)
De-zhu Li (5875247)
Kaixue Tang (6114599)
Siqing Wang (5572508)
Silan Dai (620222)
Jin-Yong Hu (3451760)

December 2018

Figure S3. Clustered heat map of expression for the nine selected Rosacaeae-common transcripts. Red ...

Additional file 4: of Comparative transcriptomics identifies patterns of selection in roses

Shubin Li (756060)
Micai Zhong (6114584)
Xue Dong (545412)
Xiaodong Jiang (456292)
Yuxing Xu (2988792)
Yibo Sun (6114593)
Fang Cheng (138729)
De-zhu Li (5875247)
Kaixue Tang (6114599)
Siqing Wang (5572508)
Silan Dai (620222)
Jin-Yong Hu (3451760)

December 2018

Table S3. KEGG and GO enrichment analysis for coreset1 transcripts. Note that each transcript could ...

Additional file 3: of Comparative transcriptomics identifies patterns of selection in roses

Shubin Li (756060)
Micai Zhong (6114584)
Xue Dong (545412)
Xiaodong Jiang (456292)
Yuxing Xu (2988792)
Yibo Sun (6114593)
Fang Cheng (138729)
De-zhu Li (5875247)
Kaixue Tang (6114599)
Siqing Wang (5572508)
Silan Dai (620222)
Jin-Yong Hu (3451760)

December 2018

Figure S1. Annotation results to Nr database. A for BT and B for OB. Transcripts of BT and OB were b...

Additional file 10: Table S10. of Transcriptomic analysis of differentially expressed genes in the floral transition of the summer flowering chrysanthemum

Liping Ren (228832)
Tao Liu (10785)
Yue Cheng (24177)
Jing Sun (141206)
Jiaojiao Gao (3460292)
Bin Dong (147019)
Sumei Chen (309431)
Fadi Chen (309436)
Jiafu Jiang (309429)

August 2016

Genes differentially transcribed in the comparison in the comparison L2 vs S2. Criteria as given in ...

Additional file 7: of Comparative transcriptomics identifies patterns of selection in roses

Shubin Li (756060)
Micai Zhong (6114584)
Xue Dong (545412)
Xiaodong Jiang (456292)
Yuxing Xu (2988792)
Yibo Sun (6114593)
Fang Cheng (138729)
De-zhu Li (5875247)
Kaixue Tang (6114599)
Siqing Wang (5572508)
Silan Dai (620222)
Jin-Yong Hu (3451760)

December 2018

Figure S2. Phylogenetic clustering of the four species based on the 4447 Rosaceae-common transcripts...

Additional file 2: of Comparative genomics and transcriptomics analysis reveals evolution patterns of selection in the Salix phylogeny

You-jie Zhao (5816699)
Xin-yi Liu (6529286)
Ran Guo (1633090)
Kun-rong Hu (6529289)
Yong Cao (9208)
Fei Dai (211873)

March 2019

Figure S1. Length distribution of transcripts in 10 Salicaceae species. (TIF 2038 kb

Additional file 10: Table S8. of Identification of mRNA isoform switching in breast cancer

Wei Zhao (14321)
Katherine Hoadley (3530135)
Joel Parker (17174)
Charles Perou (3530138)

March 2016

Significantly differentially expressed genes associated with the ratio of PRICKLE1 uc010skw.1 and uc...

Additional file 9: of Comparative Transcriptome Analysis between Fertile and CMS Flower Buds in Wucai (Brassica campestris L.)

Guohu Chen (6080591)
Xinyu Ye (401069)
Shengyun Zhang (6080594)
Shidong Zhu (6080597)
Lingyun Yuan (6080600)
Jinfeng Hou (600632)
Chenggang Wang (597525)

December 2018

Table S7. Annotation and relative expression of differentially expressed transcription factors in Wu...

Additional file 2: Table S2. of Transcriptomic analysis of differentially expressed genes in the floral transition of the summer flowering chrysanthemum

Liping Ren (228832)
Tao Liu (10785)
Yue Cheng (24177)
Jing Sun (141206)
Jiaojiao Gao (3460292)
Bin Dong (147019)
Sumei Chen (309431)
Fadi Chen (309436)
Jiafu Jiang (309429)

August 2016

The representation of transcription factors in the set of Unigenes. (XLSX 10Â kb

Additional file 1: of Comparative genomics and transcriptomics analysis reveals evolution patterns of selection in the Salix phylogeny

You-jie Zhao (5816699)
Xin-yi Liu (6529286)
Ran Guo (1633090)
Kun-rong Hu (6529289)
Yong Cao (9208)
Fei Dai (211873)

March 2019

Table S1. Main geographic distributions of 9 Salix used in this work. Table S2. Geographic distribut...

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 8: Table S3. of Transcriptome-wide functional characterization reveals novel relationships among differentially expressed transcripts in developing soybean embryos

Delasa Aghamirzaie (3550586)
Dhruv Batra (3580100)
Lenwood Heath (3580097)
Andrew Schneider (3580094)
Ruth Grene (18292)
Eva Collakova (3550583)

November 2015

Summary of all information relevant to 2,938 transcripts. This file contains the following informati...

Additional file 8: of Comparative transcriptomics identifies patterns of selection in roses

Shubin Li (756060)
Micai Zhong (6114584)
Xue Dong (545412)
Xiaodong Jiang (456292)
Yuxing Xu (2988792)
Yibo Sun (6114593)
Fang Cheng (138729)
De-zhu Li (5875247)
Kaixue Tang (6114599)
Siqing Wang (5572508)
Silan Dai (620222)
Jin-Yong Hu (3451760)

December 2018

Table S6. Raw data for the positively selected genes in the Rosaceae-common transcripts. (XLSX 185 k...

Additional file 2: of Comparative transcriptomics identifies patterns of selection in roses

Shubin Li (756060)
Micai Zhong (6114584)
Xue Dong (545412)
Xiaodong Jiang (456292)
Yuxing Xu (2988792)
Yibo Sun (6114593)
Fang Cheng (138729)
De-zhu Li (5875247)
Kaixue Tang (6114599)
Siqing Wang (5572508)
Silan Dai (620222)
Jin-Yong Hu (3451760)

December 2018

Table S2. Annotation details for both genotypes. COG, GO, KEGG, KOG, Pfam, Swissprot, TrEMBL, NR and...

Additional file 5: of Comparative transcriptomics identifies patterns of selection in roses

Shubin Li (756060)
Micai Zhong (6114584)
Xue Dong (545412)
Xiaodong Jiang (456292)
Yuxing Xu (2988792)
Yibo Sun (6114593)
Fang Cheng (138729)
De-zhu Li (5875247)
Kaixue Tang (6114599)
Siqing Wang (5572508)
Silan Dai (620222)
Jin-Yong Hu (3451760)

December 2018

Table S4. KEGG and GO clustering information of 4447 Rosaceae-common genes. (XLSX 274 kb

Additional file 11: of Comparative transcriptomics identifies patterns of selection in roses

Shubin Li (756060)
Micai Zhong (6114584)
Xue Dong (545412)
Xiaodong Jiang (456292)
Yuxing Xu (2988792)
Yibo Sun (6114593)
Fang Cheng (138729)
De-zhu Li (5875247)
Kaixue Tang (6114599)
Siqing Wang (5572508)
Silan Dai (620222)
Jin-Yong Hu (3451760)

December 2018

Figure S3. Clustered heat map of expression for the nine selected Rosacaeae-common transcripts. Red ...

Additional file 4: of Comparative transcriptomics identifies patterns of selection in roses

Shubin Li (756060)
Micai Zhong (6114584)
Xue Dong (545412)
Xiaodong Jiang (456292)
Yuxing Xu (2988792)
Yibo Sun (6114593)
Fang Cheng (138729)
De-zhu Li (5875247)
Kaixue Tang (6114599)
Siqing Wang (5572508)
Silan Dai (620222)
Jin-Yong Hu (3451760)

December 2018

Table S3. KEGG and GO enrichment analysis for coreset1 transcripts. Note that each transcript could ...

Additional file 3: of Comparative transcriptomics identifies patterns of selection in roses

Shubin Li (756060)
Micai Zhong (6114584)
Xue Dong (545412)
Xiaodong Jiang (456292)
Yuxing Xu (2988792)
Yibo Sun (6114593)
Fang Cheng (138729)
De-zhu Li (5875247)
Kaixue Tang (6114599)
Siqing Wang (5572508)
Silan Dai (620222)
Jin-Yong Hu (3451760)

December 2018

Figure S1. Annotation results to Nr database. A for BT and B for OB. Transcripts of BT and OB were b...

Additional file 10: Table S10. of Transcriptomic analysis of differentially expressed genes in the floral transition of the summer flowering chrysanthemum

Liping Ren (228832)
Tao Liu (10785)
Yue Cheng (24177)
Jing Sun (141206)
Jiaojiao Gao (3460292)
Bin Dong (147019)
Sumei Chen (309431)
Fadi Chen (309436)
Jiafu Jiang (309429)

August 2016

Genes differentially transcribed in the comparison in the comparison L2 vs S2. Criteria as given in ...

Additional file 7: of Comparative transcriptomics identifies patterns of selection in roses

Shubin Li (756060)
Micai Zhong (6114584)
Xue Dong (545412)
Xiaodong Jiang (456292)
Yuxing Xu (2988792)
Yibo Sun (6114593)
Fang Cheng (138729)
De-zhu Li (5875247)
Kaixue Tang (6114599)
Siqing Wang (5572508)
Silan Dai (620222)
Jin-Yong Hu (3451760)

December 2018

Figure S2. Phylogenetic clustering of the four species based on the 4447 Rosaceae-common transcripts...

Additional file 2: of Comparative genomics and transcriptomics analysis reveals evolution patterns of selection in the Salix phylogeny

You-jie Zhao (5816699)
Xin-yi Liu (6529286)
Ran Guo (1633090)
Kun-rong Hu (6529289)
Yong Cao (9208)
Fei Dai (211873)

March 2019

Figure S1. Length distribution of transcripts in 10 Salicaceae species. (TIF 2038 kb

Additional file 10: Table S8. of Identification of mRNA isoform switching in breast cancer

Wei Zhao (14321)
Katherine Hoadley (3530135)
Joel Parker (17174)
Charles Perou (3530138)

March 2016

Significantly differentially expressed genes associated with the ratio of PRICKLE1 uc010skw.1 and uc...

Additional file 9: of Comparative Transcriptome Analysis between Fertile and CMS Flower Buds in Wucai (Brassica campestris L.)

Guohu Chen (6080591)
Xinyu Ye (401069)
Shengyun Zhang (6080594)
Shidong Zhu (6080597)
Lingyun Yuan (6080600)
Jinfeng Hou (600632)
Chenggang Wang (597525)

December 2018

Table S7. Annotation and relative expression of differentially expressed transcription factors in Wu...

Additional file 2: Table S2. of Transcriptomic analysis of differentially expressed genes in the floral transition of the summer flowering chrysanthemum

Liping Ren (228832)
Tao Liu (10785)
Yue Cheng (24177)
Jing Sun (141206)
Jiaojiao Gao (3460292)
Bin Dong (147019)
Sumei Chen (309431)
Fadi Chen (309436)
Jiafu Jiang (309429)

August 2016

The representation of transcription factors in the set of Unigenes. (XLSX 10Â kb

Additional file 1: of Comparative genomics and transcriptomics analysis reveals evolution patterns of selection in the Salix phylogeny

You-jie Zhao (5816699)
Xin-yi Liu (6529286)
Ran Guo (1633090)
Kun-rong Hu (6529289)
Yong Cao (9208)
Fei Dai (211873)

March 2019

Table S1. Main geographic distributions of 9 Salix used in this work. Table S2. Geographic distribut...

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 8: Table S3. of Transcriptome-wide functional characterization reveals novel relationships among differentially expressed transcripts in developing soybean embryos

Delasa Aghamirzaie (3550586)
Dhruv Batra (3580100)
Lenwood Heath (3580097)
Andrew Schneider (3580094)
Ruth Grene (18292)
Eva Collakova (3550583)

November 2015

Summary of all information relevant to 2,938 transcripts. This file contains the following informati...

Additional file 10: of Comparative transcriptomics identifies patterns of selection in roses

Abstract

Extracted data

Additional file 10: of Comparative transcriptomics identifies patterns of selection in roses

Abstract

Extracted data

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