Additional file 9: of Transcriptome dynamics of rooting zone and aboveground parts of cuttings during adventitious root formation in Cryptomeria japonica D. Don

Additional file 4: Figure S2. of Gene expression profiling during adventitious root formation in carnation stem cuttings

Carlos Villacorta-Martín (3500351)
Ana Sánchez-García (3500345)
Joan Villanova (778244)
Antonio Cano (103418)
Miranda van de Rhee (3500357)
Jorn de Haan (3421820)
Manuel Acosta (52993)
Paul Passarinho (3500354)
José Pérez-Pérez (3500348)

October 2015

Validation of RNA-seq results by qRT-PCR. The relative expression of six genes was studied in the 20...

Additional file 8: of Parallel evolution of storage roots in morning glories (Convolvulaceae)

Lauren Eserman (5315306)
Robert Jarret (5315309)
James Leebens-Mack (117283)

May 2018

Table S8. Functional annotation of genes and transcripts in Ipomoea batatas from Trinotate. (XLSX 12...

Additional file 2: Table S2. of Poplar stem transcriptome is massively remodelled in response to single or repeated mechanical stimuli

Lise Pomiès (3928364)
Mélanie Decourteix (3928370)
Jérôme Franchel (3928361)
Bruno Moulia (693150)
Nathalie Leblanc-Fournier (3928367)

April 2017

List of the 10 most up- or down-regulated genes at each time-point. *gene_ID corresponds to the gene...

Additional file 5: of Transcriptome dynamics of rooting zone and aboveground parts of cuttings during adventitious root formation in Cryptomeria japonica D. Don

Yuki Fukuda (1503802)
Tomonori Hirao (64182)
Kentaro Mishima (487195)
Mineko Ohira (3763561)
Yuichiro Hiraoka (5736059)
Makoto Takahashi (386772)
Atsushi Watanabe (64183)

September 2018

Table S2. Annotation of genes in clusters in (A) “all”, (B) “base and middle” and (C) “needles”. (XL...

Additional file 8: of Transcriptome dynamics of rooting zone and aboveground parts of cuttings during adventitious root formation in Cryptomeria japonica D. Don

Yuki Fukuda (1503802)
Tomonori Hirao (64182)
Kentaro Mishima (487195)
Mineko Ohira (3763561)
Yuichiro Hiraoka (5736059)
Makoto Takahashi (386772)
Atsushi Watanabe (64183)

September 2018

Table S5. Functional enrichment annotations for the top 100 genes with the largest PC1. (XLSX 10 kb

Additional file 6: of Transcriptome dynamics of rooting zone and aboveground parts of cuttings during adventitious root formation in Cryptomeria japonica D. Don

Yuki Fukuda (1503802)
Tomonori Hirao (64182)
Kentaro Mishima (487195)
Mineko Ohira (3763561)
Yuichiro Hiraoka (5736059)
Makoto Takahashi (386772)
Atsushi Watanabe (64183)

September 2018

Table S3. Functional annotation in clusters in (A) “all”, (B) “base and middle” and (C) “needles”. (...

Additional file 7: of Transcriptome dynamics of rooting zone and aboveground parts of cuttings during adventitious root formation in Cryptomeria japonica D. Don

Yuki Fukuda (1503802)
Tomonori Hirao (64182)
Kentaro Mishima (487195)
Mineko Ohira (3763561)
Yuichiro Hiraoka (5736059)
Makoto Takahashi (386772)
Atsushi Watanabe (64183)

September 2018

Table S4. Annotation of the top 100 genes with the largest principal component 1 (PC1) coefficients....

Additional file 2: of Transcriptome dynamics of rooting zone and aboveground parts of cuttings during adventitious root formation in Cryptomeria japonica D. Don

Yuki Fukuda (1503802)
Tomonori Hirao (64182)
Kentaro Mishima (487195)
Mineko Ohira (3763561)
Yuichiro Hiraoka (5736059)
Makoto Takahashi (386772)
Atsushi Watanabe (64183)

September 2018

Figure S2. Validation of microarray data by qRT-PCR in the middle. Bars represent the means Âą stand...

Additional file 1: of Transcriptome dynamics of rooting zone and aboveground parts of cuttings during adventitious root formation in Cryptomeria japonica D. Don

Yuki Fukuda (1503802)
Tomonori Hirao (64182)
Kentaro Mishima (487195)
Mineko Ohira (3763561)
Yuichiro Hiraoka (5736059)
Makoto Takahashi (386772)
Atsushi Watanabe (64183)

September 2018

Figure S1. Validation of microarray data by qRT-PCR at the base. Bars represent the means Âą standar...

Additional file 3: of Transcriptome dynamics of rooting zone and aboveground parts of cuttings during adventitious root formation in Cryptomeria japonica D. Don

Yuki Fukuda (1503802)
Tomonori Hirao (64182)
Kentaro Mishima (487195)
Mineko Ohira (3763561)
Yuichiro Hiraoka (5736059)
Makoto Takahashi (386772)
Atsushi Watanabe (64183)

September 2018

Figure S3. Validation of microarray data by qRT-PCR in needles. Bars represent the means Âą standard...

Transcriptome dynamics of rooting zone and aboveground parts of cuttings during adventitious root formation in Cryptomeria japonica D. Don

Yuki Fukuda
Tomonori Hirao
Kentaro Mishima
Mineko Ohira
Yuichiro Hiraoka
Makoto Takahashi
Atsushi Watanabe

September 2018

Abstract Background Adventitious root formation is an essential physiological process for successful...

Additional file 1: of Integration of genetic, genomic and transcriptomic information identifies putative regulators of adventitious root formation in Populus

Cintia Ribeiro (3472373)
Cynthia Silva (3424709)
Derek Drost (3472379)
Evandro Novaes (91543)
Carolina Novaes (3472376)
Christopher Dervinis (3472370)
Matias Kirst (91546)

March 2016

Cumulative number of roots formed in the parents of pedigree 52–124. Least-square means of number of...

Additional file 9: of Dynamics of the Phanerochaete carnosa transcriptome during growth on aspen and spruce

E. Jurak (5961617)
H. Suzuki (3008037)
G. van Erven (5961620)
J. Gandier (5961623)
P. Wong (5961626)
K. Chan (5068958)
C. Ho (5961629)
Y. Gong (70953)
E. Tillier (5961632)
M.-N. Rosso (5961635)
M. Kabel (3995177)
S. Miyauchi (5961638)
E. Master (5961641)

November 2018

The distribution and density of normalized log2 transformed read counts of 11,796 genes from 10 cond...

Additional file 9: of Parallel evolution of storage roots in morning glories (Convolvulaceae)

Lauren Eserman (5315306)
Robert Jarret (5315309)
James Leebens-Mack (117283)

May 2018

Table S9. Functional annotation of genes and transcripts in Ipomoea trifida from Trinotate. (XLSX 10...

Additional file 8: of Dynamics of the Phanerochaete carnosa transcriptome during growth on aspen and spruce

E. Jurak (5961617)
H. Suzuki (3008037)
G. van Erven (5961620)
J. Gandier (5961623)
P. Wong (5961626)
K. Chan (5068958)
C. Ho (5961629)
Y. Gong (70953)
E. Tillier (5961632)
M.-N. Rosso (5961635)
M. Kabel (3995177)
S. Miyauchi (5961638)
E. Master (5961641)

November 2018

The annotations per protein IDs in 480 nodes. The nodes with high/differential transcriptions are la...

Additional file 4: Figure S2. of Gene expression profiling during adventitious root formation in carnation stem cuttings

Carlos Villacorta-Martín (3500351)
Ana Sánchez-García (3500345)
Joan Villanova (778244)
Antonio Cano (103418)
Miranda van de Rhee (3500357)
Jorn de Haan (3421820)
Manuel Acosta (52993)
Paul Passarinho (3500354)
José Pérez-Pérez (3500348)

October 2015

Validation of RNA-seq results by qRT-PCR. The relative expression of six genes was studied in the 20...

Additional file 8: of Parallel evolution of storage roots in morning glories (Convolvulaceae)

Lauren Eserman (5315306)
Robert Jarret (5315309)
James Leebens-Mack (117283)

May 2018

Table S8. Functional annotation of genes and transcripts in Ipomoea batatas from Trinotate. (XLSX 12...

Additional file 2: Table S2. of Poplar stem transcriptome is massively remodelled in response to single or repeated mechanical stimuli

Lise Pomiès (3928364)
Mélanie Decourteix (3928370)
Jérôme Franchel (3928361)
Bruno Moulia (693150)
Nathalie Leblanc-Fournier (3928367)

April 2017

List of the 10 most up- or down-regulated genes at each time-point. *gene_ID corresponds to the gene...

Additional file 5: of Transcriptome dynamics of rooting zone and aboveground parts of cuttings during adventitious root formation in Cryptomeria japonica D. Don

Yuki Fukuda (1503802)
Tomonori Hirao (64182)
Kentaro Mishima (487195)
Mineko Ohira (3763561)
Yuichiro Hiraoka (5736059)
Makoto Takahashi (386772)
Atsushi Watanabe (64183)

September 2018

Table S2. Annotation of genes in clusters in (A) “all”, (B) “base and middle” and (C) “needles”. (XL...

Additional file 8: of Transcriptome dynamics of rooting zone and aboveground parts of cuttings during adventitious root formation in Cryptomeria japonica D. Don

Yuki Fukuda (1503802)
Tomonori Hirao (64182)
Kentaro Mishima (487195)
Mineko Ohira (3763561)
Yuichiro Hiraoka (5736059)
Makoto Takahashi (386772)
Atsushi Watanabe (64183)

September 2018

Table S5. Functional enrichment annotations for the top 100 genes with the largest PC1. (XLSX 10 kb

Additional file 6: of Transcriptome dynamics of rooting zone and aboveground parts of cuttings during adventitious root formation in Cryptomeria japonica D. Don

Yuki Fukuda (1503802)
Tomonori Hirao (64182)
Kentaro Mishima (487195)
Mineko Ohira (3763561)
Yuichiro Hiraoka (5736059)
Makoto Takahashi (386772)
Atsushi Watanabe (64183)

September 2018

Table S3. Functional annotation in clusters in (A) “all”, (B) “base and middle” and (C) “needles”. (...

Additional file 7: of Transcriptome dynamics of rooting zone and aboveground parts of cuttings during adventitious root formation in Cryptomeria japonica D. Don

Yuki Fukuda (1503802)
Tomonori Hirao (64182)
Kentaro Mishima (487195)
Mineko Ohira (3763561)
Yuichiro Hiraoka (5736059)
Makoto Takahashi (386772)
Atsushi Watanabe (64183)

September 2018

Table S4. Annotation of the top 100 genes with the largest principal component 1 (PC1) coefficients....

Additional file 2: of Transcriptome dynamics of rooting zone and aboveground parts of cuttings during adventitious root formation in Cryptomeria japonica D. Don

Yuki Fukuda (1503802)
Tomonori Hirao (64182)
Kentaro Mishima (487195)
Mineko Ohira (3763561)
Yuichiro Hiraoka (5736059)
Makoto Takahashi (386772)
Atsushi Watanabe (64183)

September 2018

Figure S2. Validation of microarray data by qRT-PCR in the middle. Bars represent the means Âą stand...

Additional file 1: of Transcriptome dynamics of rooting zone and aboveground parts of cuttings during adventitious root formation in Cryptomeria japonica D. Don

Yuki Fukuda (1503802)
Tomonori Hirao (64182)
Kentaro Mishima (487195)
Mineko Ohira (3763561)
Yuichiro Hiraoka (5736059)
Makoto Takahashi (386772)
Atsushi Watanabe (64183)

September 2018

Figure S1. Validation of microarray data by qRT-PCR at the base. Bars represent the means Âą standar...

Additional file 3: of Transcriptome dynamics of rooting zone and aboveground parts of cuttings during adventitious root formation in Cryptomeria japonica D. Don

Yuki Fukuda (1503802)
Tomonori Hirao (64182)
Kentaro Mishima (487195)
Mineko Ohira (3763561)
Yuichiro Hiraoka (5736059)
Makoto Takahashi (386772)
Atsushi Watanabe (64183)

September 2018

Figure S3. Validation of microarray data by qRT-PCR in needles. Bars represent the means Âą standard...

Transcriptome dynamics of rooting zone and aboveground parts of cuttings during adventitious root formation in Cryptomeria japonica D. Don

Yuki Fukuda
Tomonori Hirao
Kentaro Mishima
Mineko Ohira
Yuichiro Hiraoka
Makoto Takahashi
Atsushi Watanabe

September 2018

Abstract Background Adventitious root formation is an essential physiological process for successful...

Additional file 1: of Integration of genetic, genomic and transcriptomic information identifies putative regulators of adventitious root formation in Populus

Cintia Ribeiro (3472373)
Cynthia Silva (3424709)
Derek Drost (3472379)
Evandro Novaes (91543)
Carolina Novaes (3472376)
Christopher Dervinis (3472370)
Matias Kirst (91546)

March 2016

Cumulative number of roots formed in the parents of pedigree 52–124. Least-square means of number of...

Additional file 9: of Dynamics of the Phanerochaete carnosa transcriptome during growth on aspen and spruce

E. Jurak (5961617)
H. Suzuki (3008037)
G. van Erven (5961620)
J. Gandier (5961623)
P. Wong (5961626)
K. Chan (5068958)
C. Ho (5961629)
Y. Gong (70953)
E. Tillier (5961632)
M.-N. Rosso (5961635)
M. Kabel (3995177)
S. Miyauchi (5961638)
E. Master (5961641)

November 2018

The distribution and density of normalized log2 transformed read counts of 11,796 genes from 10 cond...

Additional file 9: of Parallel evolution of storage roots in morning glories (Convolvulaceae)

Lauren Eserman (5315306)
Robert Jarret (5315309)
James Leebens-Mack (117283)

May 2018

Table S9. Functional annotation of genes and transcripts in Ipomoea trifida from Trinotate. (XLSX 10...

Additional file 8: of Dynamics of the Phanerochaete carnosa transcriptome during growth on aspen and spruce

E. Jurak (5961617)
H. Suzuki (3008037)
G. van Erven (5961620)
J. Gandier (5961623)
P. Wong (5961626)
K. Chan (5068958)
C. Ho (5961629)
Y. Gong (70953)
E. Tillier (5961632)
M.-N. Rosso (5961635)
M. Kabel (3995177)
S. Miyauchi (5961638)
E. Master (5961641)

November 2018

The annotations per protein IDs in 480 nodes. The nodes with high/differential transcriptions are la...

Additional file 4: Figure S2. of Gene expression profiling during adventitious root formation in carnation stem cuttings

Carlos Villacorta-Martín (3500351)
Ana Sánchez-García (3500345)
Joan Villanova (778244)
Antonio Cano (103418)
Miranda van de Rhee (3500357)
Jorn de Haan (3421820)
Manuel Acosta (52993)
Paul Passarinho (3500354)
José Pérez-Pérez (3500348)

October 2015

Validation of RNA-seq results by qRT-PCR. The relative expression of six genes was studied in the 20...

Additional file 8: of Parallel evolution of storage roots in morning glories (Convolvulaceae)

Lauren Eserman (5315306)
Robert Jarret (5315309)
James Leebens-Mack (117283)

May 2018

Table S8. Functional annotation of genes and transcripts in Ipomoea batatas from Trinotate. (XLSX 12...

Additional file 2: Table S2. of Poplar stem transcriptome is massively remodelled in response to single or repeated mechanical stimuli

Lise Pomiès (3928364)
Mélanie Decourteix (3928370)
Jérôme Franchel (3928361)
Bruno Moulia (693150)
Nathalie Leblanc-Fournier (3928367)

April 2017

List of the 10 most up- or down-regulated genes at each time-point. *gene_ID corresponds to the gene...

Additional file 9: of Transcriptome dynamics of rooting zone and aboveground parts of cuttings during adventitious root formation in Cryptomeria japonica D. Don

Abstract

Extracted data

Additional file 9: of Transcriptome dynamics of rooting zone and aboveground parts of cuttings during adventitious root formation in Cryptomeria japonica D. Don

Abstract

Extracted data

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