Additional file 7: of Characterization of siRNAs clusters in Arabidopsis thaliana galls induced by the root-knot nematode Meloidogyne incognita

Additional file 8: of Genome-wide expert annotation of the epigenetic machinery of the plant-parasitic nematodes Meloidogyne spp., with a focus on the asexuallyÂ reproducing species

Loris Pratx (5173871)
Corinne Rancurel (47753)
Martine Da Rocha (115956)
Etienne Danchin (2912072)
Philippe Castagnone-Sereno (158157)
Pierre Abad (115959)
Laetitia Perfus-Barbeoch (478461)

May 2018

Table S6. Complete list of histones and histone modifying enzymes annotation. In the 6 model species...

Additional file 1: of STATAWAARS: a promoter motif associated with spatial expression in the major effector-producing tissues of the plant-parasitic nematode Bursaphelenchus xylophilus

Margarida Espada (302655)
Sebastian Eves-van den Akker (515790)
Tom Maier (5567603)
Vijayapalani Paramasivan (5567606)
Thomas Baum (406296)
Manuel Mota (281005)
John Jones (2102023)

July 2018

Table S1. List of verified effector genes from Bursaphelenchus xylophilus used for the analysis of t...

Additional file 3: of STATAWAARS: a promoter motif associated with spatial expression in the major effector-producing tissues of the plant-parasitic nematode Bursaphelenchus xylophilus

Margarida Espada (302655)
Sebastian Eves-van den Akker (515790)
Tom Maier (5567603)
Vijayapalani Paramasivan (5567606)
Thomas Baum (406296)
Manuel Mota (281005)
John Jones (2102023)

July 2018

Table S3. RNAseq mapped data from the two samples sequenced (BX-1, BX-2). (PDF 22 kb

Additional file 8: of Characterization of siRNAs clusters in Arabidopsis thaliana galls induced by the root-knot nematode Meloidogyne incognita

ClĂŠmence Medina (6100826)
Martine da Rocha (6100817)
Marc Magliano (223262)
AlizĂŠe Raptopoulo (6100829)
Nathalie Marteu (6100823)
Kevin Lebrigand (138002)
Pierre Abad (115959)
Bruno Favery (190085)
StĂŠphanie Jaubert-Possamai (6100832)

December 2018

Table S7 List of DC-clusters differentially expressed (DE) in galls versus uninfected roots at 14 dp...

Additional file 9: of Characterization of siRNAs clusters in Arabidopsis thaliana galls induced by the root-knot nematode Meloidogyne incognita

ClĂŠmence Medina (6100826)
Martine da Rocha (6100817)
Marc Magliano (223262)
AlizĂŠe Raptopoulo (6100829)
Nathalie Marteu (6100823)
Kevin Lebrigand (138002)
Pierre Abad (115959)
Bruno Favery (190085)
StĂŠphanie Jaubert-Possamai (6100832)

December 2018

Table S8. List of DC-clusters differentially expressed (DE) in galls versus uninfected root at 7 and...

Additional file 6: of Characterization of siRNAs clusters in Arabidopsis thaliana galls induced by the root-knot nematode Meloidogyne incognita

ClĂŠmence Medina (6100826)
Martine da Rocha (6100817)
Marc Magliano (223262)
AlizĂŠe Raptopoulo (6100829)
Nathalie Marteu (6100823)
Kevin Lebrigand (138002)
Pierre Abad (115959)
Bruno Favery (190085)
StĂŠphanie Jaubert-Possamai (6100832)

December 2018

Table S5. Number and proportion of differentially expressed (DE) DC-clusters located in a gene body ...

Additional file 4: of Characterization of siRNAs clusters in Arabidopsis thaliana galls induced by the root-knot nematode Meloidogyne incognita

ClĂŠmence Medina (6100826)
Martine da Rocha (6100817)
Marc Magliano (223262)
AlizĂŠe Raptopoulo (6100829)
Nathalie Marteu (6100823)
Kevin Lebrigand (138002)
Pierre Abad (115959)
Bruno Favery (190085)
StĂŠphanie Jaubert-Possamai (6100832)

December 2018

Table S3. Lists of DC-clusters differentially expressed in galls at 7 and 14 dpi and located within ...

Additional file 5: of Characterization of siRNAs clusters in Arabidopsis thaliana galls induced by the root-knot nematode Meloidogyne incognita

ClĂŠmence Medina (6100826)
Martine da Rocha (6100817)
Marc Magliano (223262)
AlizĂŠe Raptopoulo (6100829)
Nathalie Marteu (6100823)
Kevin Lebrigand (138002)
Pierre Abad (115959)
Bruno Favery (190085)
StĂŠphanie Jaubert-Possamai (6100832)

December 2018

Table S4. Lists of DC-clusters exclusively expressed in galls or roots at 7 and 14 dpi and located w...

Additional file 3: of Characterization of siRNAs clusters in Arabidopsis thaliana galls induced by the root-knot nematode Meloidogyne incognita

ClĂŠmence Medina (6100826)
Martine da Rocha (6100817)
Marc Magliano (223262)
AlizĂŠe Raptopoulo (6100829)
Nathalie Marteu (6100823)
Kevin Lebrigand (138002)
Pierre Abad (115959)
Bruno Favery (190085)
StĂŠphanie Jaubert-Possamai (6100832)

December 2018

Table S2. Selection of clusters differentially expressed (DE) in galls at 7 and 14dpi. (XLSX 12 kb

Additional file 1: of Characterization of siRNAs clusters in Arabidopsis thaliana galls induced by the root-knot nematode Meloidogyne incognita

Clémence Medina (6100814)
Martine da Rocha (6100817)
Marc Magliano (223262)
Alizée Raptopoulo (6100820)
Nathalie Marteu (6100823)
Kevin Lebrigand (138002)
Pierre Abad (115959)
Bruno Favery (190085)
Stéphanie Jaubert-Possamai (36467)

December 2018

Figure S1. Percentage of reads of 20, 21, 22, 23, 24 nt within each category of DicerCall clusters i...

Additional file 5: of STATAWAARS: a promoter motif associated with spatial expression in the major effector-producing tissues of the plant-parasitic nematode Bursaphelenchus xylophilus

Margarida Espada (302655)
Sebastian Eves-van den Akker (515790)
Tom Maier (5567603)
Vijayapalani Paramasivan (5567606)
Thomas Baum (406296)
Manuel Mota (281005)
John Jones (2102023)

July 2018

Table S5. Limited overlap (venny diagram) between the top most abundant thirty genes represented in ...

Additional file 6: of STATAWAARS: a promoter motif associated with spatial expression in the major effector-producing tissues of the plant-parasitic nematode Bursaphelenchus xylophilus

Margarida Espada (302655)
Sebastian Eves-van den Akker (515790)
Tom Maier (5567603)
Vijayapalani Paramasivan (5567606)
Thomas Baum (406296)
Manuel Mota (281005)
John Jones (2102023)

July 2018

Table S6. Bioinformatic pipeline used for the in silico identification of DNA motifs in the promoter...

Additional file 4: Figure S1. 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

Clustering of differentially expressed genes based on expression patterns relative to time of inocul...

Additional file 14: of Rice stripe virus-derived siRNAs play different regulatory roles in rice and in the insect vector Laodelphax striatellus

Meiling Yang (153319)
Zhongtian Xu (5820452)
Wan Zhao (390898)
Qing Liu (20889)
Qiong Li (346270)
Lu Lu (392)
Renyi Liu (92885)
Xiaoming Zhang (104062)
Feng Cui (23907)

October 2018

Figure S11. Volcano plot to show the fold change and error rates of differentially expressed genes (...

Additional file 7: of STATAWAARS: a promoter motif associated with spatial expression in the major effector-producing tissues of the plant-parasitic nematode Bursaphelenchus xylophilus

Margarida Espada (302655)
Sebastian Eves-van den Akker (515790)
Tom Maier (5567603)
Vijayapalani Paramasivan (5567606)
Thomas Baum (406296)
Manuel Mota (281005)
John Jones (2102023)

July 2018

Table S7. List of ten genes that have the presence of STATAWAARS motif and where selected to examine...

Additional file 8: of Genome-wide expert annotation of the epigenetic machinery of the plant-parasitic nematodes Meloidogyne spp., with a focus on the asexuallyÂ reproducing species

Loris Pratx (5173871)
Corinne Rancurel (47753)
Martine Da Rocha (115956)
Etienne Danchin (2912072)
Philippe Castagnone-Sereno (158157)
Pierre Abad (115959)
Laetitia Perfus-Barbeoch (478461)

May 2018

Table S6. Complete list of histones and histone modifying enzymes annotation. In the 6 model species...

Additional file 1: of STATAWAARS: a promoter motif associated with spatial expression in the major effector-producing tissues of the plant-parasitic nematode Bursaphelenchus xylophilus

Margarida Espada (302655)
Sebastian Eves-van den Akker (515790)
Tom Maier (5567603)
Vijayapalani Paramasivan (5567606)
Thomas Baum (406296)
Manuel Mota (281005)
John Jones (2102023)

July 2018

Table S1. List of verified effector genes from Bursaphelenchus xylophilus used for the analysis of t...

Additional file 3: of STATAWAARS: a promoter motif associated with spatial expression in the major effector-producing tissues of the plant-parasitic nematode Bursaphelenchus xylophilus

Margarida Espada (302655)
Sebastian Eves-van den Akker (515790)
Tom Maier (5567603)
Vijayapalani Paramasivan (5567606)
Thomas Baum (406296)
Manuel Mota (281005)
John Jones (2102023)

July 2018

Table S3. RNAseq mapped data from the two samples sequenced (BX-1, BX-2). (PDF 22 kb

Additional file 8: of Characterization of siRNAs clusters in Arabidopsis thaliana galls induced by the root-knot nematode Meloidogyne incognita

ClĂŠmence Medina (6100826)
Martine da Rocha (6100817)
Marc Magliano (223262)
AlizĂŠe Raptopoulo (6100829)
Nathalie Marteu (6100823)
Kevin Lebrigand (138002)
Pierre Abad (115959)
Bruno Favery (190085)
StĂŠphanie Jaubert-Possamai (6100832)

December 2018

Table S7 List of DC-clusters differentially expressed (DE) in galls versus uninfected roots at 14 dp...

Additional file 9: of Characterization of siRNAs clusters in Arabidopsis thaliana galls induced by the root-knot nematode Meloidogyne incognita

ClĂŠmence Medina (6100826)
Martine da Rocha (6100817)
Marc Magliano (223262)
AlizĂŠe Raptopoulo (6100829)
Nathalie Marteu (6100823)
Kevin Lebrigand (138002)
Pierre Abad (115959)
Bruno Favery (190085)
StĂŠphanie Jaubert-Possamai (6100832)

December 2018

Table S8. List of DC-clusters differentially expressed (DE) in galls versus uninfected root at 7 and...

Additional file 6: of Characterization of siRNAs clusters in Arabidopsis thaliana galls induced by the root-knot nematode Meloidogyne incognita

ClĂŠmence Medina (6100826)
Martine da Rocha (6100817)
Marc Magliano (223262)
AlizĂŠe Raptopoulo (6100829)
Nathalie Marteu (6100823)
Kevin Lebrigand (138002)
Pierre Abad (115959)
Bruno Favery (190085)
StĂŠphanie Jaubert-Possamai (6100832)

December 2018

Table S5. Number and proportion of differentially expressed (DE) DC-clusters located in a gene body ...

Additional file 4: of Characterization of siRNAs clusters in Arabidopsis thaliana galls induced by the root-knot nematode Meloidogyne incognita

ClĂŠmence Medina (6100826)
Martine da Rocha (6100817)
Marc Magliano (223262)
AlizĂŠe Raptopoulo (6100829)
Nathalie Marteu (6100823)
Kevin Lebrigand (138002)
Pierre Abad (115959)
Bruno Favery (190085)
StĂŠphanie Jaubert-Possamai (6100832)

December 2018

Table S3. Lists of DC-clusters differentially expressed in galls at 7 and 14 dpi and located within ...

Additional file 5: of Characterization of siRNAs clusters in Arabidopsis thaliana galls induced by the root-knot nematode Meloidogyne incognita

ClĂŠmence Medina (6100826)
Martine da Rocha (6100817)
Marc Magliano (223262)
AlizĂŠe Raptopoulo (6100829)
Nathalie Marteu (6100823)
Kevin Lebrigand (138002)
Pierre Abad (115959)
Bruno Favery (190085)
StĂŠphanie Jaubert-Possamai (6100832)

December 2018

Table S4. Lists of DC-clusters exclusively expressed in galls or roots at 7 and 14 dpi and located w...

Additional file 3: of Characterization of siRNAs clusters in Arabidopsis thaliana galls induced by the root-knot nematode Meloidogyne incognita

ClĂŠmence Medina (6100826)
Martine da Rocha (6100817)
Marc Magliano (223262)
AlizĂŠe Raptopoulo (6100829)
Nathalie Marteu (6100823)
Kevin Lebrigand (138002)
Pierre Abad (115959)
Bruno Favery (190085)
StĂŠphanie Jaubert-Possamai (6100832)

December 2018

Table S2. Selection of clusters differentially expressed (DE) in galls at 7 and 14dpi. (XLSX 12 kb

Additional file 1: of Characterization of siRNAs clusters in Arabidopsis thaliana galls induced by the root-knot nematode Meloidogyne incognita

Clémence Medina (6100814)
Martine da Rocha (6100817)
Marc Magliano (223262)
Alizée Raptopoulo (6100820)
Nathalie Marteu (6100823)
Kevin Lebrigand (138002)
Pierre Abad (115959)
Bruno Favery (190085)
Stéphanie Jaubert-Possamai (36467)

December 2018

Figure S1. Percentage of reads of 20, 21, 22, 23, 24 nt within each category of DicerCall clusters i...

Additional file 5: of STATAWAARS: a promoter motif associated with spatial expression in the major effector-producing tissues of the plant-parasitic nematode Bursaphelenchus xylophilus

Margarida Espada (302655)
Sebastian Eves-van den Akker (515790)
Tom Maier (5567603)
Vijayapalani Paramasivan (5567606)
Thomas Baum (406296)
Manuel Mota (281005)
John Jones (2102023)

July 2018

Table S5. Limited overlap (venny diagram) between the top most abundant thirty genes represented in ...

Additional file 6: of STATAWAARS: a promoter motif associated with spatial expression in the major effector-producing tissues of the plant-parasitic nematode Bursaphelenchus xylophilus

Margarida Espada (302655)
Sebastian Eves-van den Akker (515790)
Tom Maier (5567603)
Vijayapalani Paramasivan (5567606)
Thomas Baum (406296)
Manuel Mota (281005)
John Jones (2102023)

July 2018

Table S6. Bioinformatic pipeline used for the in silico identification of DNA motifs in the promoter...

Additional file 4: Figure S1. 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

Clustering of differentially expressed genes based on expression patterns relative to time of inocul...

Additional file 14: of Rice stripe virus-derived siRNAs play different regulatory roles in rice and in the insect vector Laodelphax striatellus

Meiling Yang (153319)
Zhongtian Xu (5820452)
Wan Zhao (390898)
Qing Liu (20889)
Qiong Li (346270)
Lu Lu (392)
Renyi Liu (92885)
Xiaoming Zhang (104062)
Feng Cui (23907)

October 2018

Figure S11. Volcano plot to show the fold change and error rates of differentially expressed genes (...

Additional file 7: of STATAWAARS: a promoter motif associated with spatial expression in the major effector-producing tissues of the plant-parasitic nematode Bursaphelenchus xylophilus

Margarida Espada (302655)
Sebastian Eves-van den Akker (515790)
Tom Maier (5567603)
Vijayapalani Paramasivan (5567606)
Thomas Baum (406296)
Manuel Mota (281005)
John Jones (2102023)

July 2018

Table S7. List of ten genes that have the presence of STATAWAARS motif and where selected to examine...

Additional file 8: of Genome-wide expert annotation of the epigenetic machinery of the plant-parasitic nematodes Meloidogyne spp., with a focus on the asexuallyÂ reproducing species

Loris Pratx (5173871)
Corinne Rancurel (47753)
Martine Da Rocha (115956)
Etienne Danchin (2912072)
Philippe Castagnone-Sereno (158157)
Pierre Abad (115959)
Laetitia Perfus-Barbeoch (478461)

May 2018

Table S6. Complete list of histones and histone modifying enzymes annotation. In the 6 model species...

Additional file 1: of STATAWAARS: a promoter motif associated with spatial expression in the major effector-producing tissues of the plant-parasitic nematode Bursaphelenchus xylophilus

Margarida Espada (302655)
Sebastian Eves-van den Akker (515790)
Tom Maier (5567603)
Vijayapalani Paramasivan (5567606)
Thomas Baum (406296)
Manuel Mota (281005)
John Jones (2102023)

July 2018

Table S1. List of verified effector genes from Bursaphelenchus xylophilus used for the analysis of t...

Additional file 3: of STATAWAARS: a promoter motif associated with spatial expression in the major effector-producing tissues of the plant-parasitic nematode Bursaphelenchus xylophilus

Margarida Espada (302655)
Sebastian Eves-van den Akker (515790)
Tom Maier (5567603)
Vijayapalani Paramasivan (5567606)
Thomas Baum (406296)
Manuel Mota (281005)
John Jones (2102023)

July 2018

Table S3. RNAseq mapped data from the two samples sequenced (BX-1, BX-2). (PDF 22 kb

Additional file 7: of Characterization of siRNAs clusters in Arabidopsis thaliana galls induced by the root-knot nematode Meloidogyne incognita

Abstract

Extracted data

Additional file 7: of Characterization of siRNAs clusters in Arabidopsis thaliana galls induced by the root-knot nematode Meloidogyne incognita

Abstract

Extracted data

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