Additional file 6: Table S5. of Reciprocal changes in DNA methylation and hydroxymethylation and a broad repressive epigenetic switch characterize FMR1 transcriptional silencing in fragile X syndrome

Sarah Brasa (226861)
Arne Mueller (3518105)
SĂŠbastien Jacquemont (3518102)
Florian Hahne (14246)
Izabela Rozenberg (214521)
Thomas Peters (147287)
Yunsheng He (3518108)
Christine McCormack (3518111)
Fabrizio Gasparini (3011970)
Salah-Dine Chibout (370640)
Olivier Grenet (106357)
Jonathan Moggs (147210)
Baltazar Gomez-Mancilla (3518099)
RĂŠmi Terranova (3518096)

Publication date

February 2016

DOI

10.6084/m9.figshare.c.3626552_d6.v1

Abstract

This table summarizes linear regression analyses (p value, RSq, R) for the indicated molecular assay (5mC, 5hmC, histone PTMs). (XLSX 128Â kb

Extracted data

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Additional file 6: Table S5. of Reciprocal changes in DNA methylation and hydroxymethylation and a broad repressive epigenetic switch characterize FMR1 transcriptional silencing in fragile X syndrome

Sarah Brasa (226861)
Arne Mueller (3518105)
SĂŠbastien Jacquemont (3518102)
Florian Hahne (14246)
Izabela Rozenberg (214521)
Thomas Peters (147287)
Yunsheng He (3518108)
Christine McCormack (3518111)
Fabrizio Gasparini (3011970)
Salah-Dine Chibout (370640)
Olivier Grenet (106357)
Jonathan Moggs (147210)
Baltazar Gomez-Mancilla (3518099)
RĂŠmi Terranova (3518096)

Open link

Publication date

February 2016

DOI

10.6084/m9.figshare.c.3626552_d6.v1

Abstract

This table summarizes linear regression analyses (p value, RSq, R) for the indicated molecular assay (5mC, 5hmC, histone PTMs). (XLSX 128Â kb

Extracted data

Rong Yang (107028)
Zhimin Zheng (436481)
Qing Chen (131379)
Lan Yang (457660)
Huan Huang (724980)
Daisuke Miki (105782)
Wenwu Wu (196470)
Liang Zeng (791005)
Jun Liu (42548)
Jin-Xing Zhou (167426)
Joe Ogas (4058497)
Jian-Kang Zhu (23700)
Xin-Jian He (167435)
Heng Zhang (320479)

May 2017

Statistics of RNA-seq data. Table S2. List of differentially expressed genes in the pkl mutant ident...

Additional file 5: of A pan-cancer analysis of driver gene mutations, DNA methylation and gene expressions reveals that chromatin remodeling is a major mechanism inducing global changes in cancer epigenomes

Ahrim Youn (4606252)
Kyung In Kim (47502)
Raul Rabadan (88130)
Benjamin Tycko (237065)
Yufeng Shen (239573)
Shuang Wang (46453)

November 2018

Table S4. CDGs associated with significant genome-wide methylation changes in one cancer type. Hyper...

Additional file 9: Table S2. of Reciprocal changes in DNA methylation and hydroxymethylation and a broad repressive epigenetic switch characterize FMR1 transcriptional silencing in fragile X syndrome

Sarah Brasa (226861)
Arne Mueller (3518105)
SĂŠbastien Jacquemont (3518102)
Florian Hahne (14246)
Izabela Rozenberg (214521)
Thomas Peters (147287)
Yunsheng He (3518108)
Christine McCormack (3518111)
Fabrizio Gasparini (3011970)
Salah-Dine Chibout (370640)
Olivier Grenet (106357)
Jonathan Moggs (147210)
Baltazar Gomez-Mancilla (3518099)
RĂŠmi Terranova (3518096)

February 2016

List of the real-time qPCR assays. This table indicates the primers sequence as well as chromosome c...

Additional file 3: Figure S2. of Reciprocal changes in DNA methylation and hydroxymethylation and a broad repressive epigenetic switch characterize FMR1 transcriptional silencing in fragile X syndrome

Sarah Brasa (226861)
Arne Mueller (3518105)
Sébastien Jacquemont (3518123)
Florian Hahne (14246)
Izabela Rozenberg (214521)
Thomas Peters (147287)
Yunsheng He (3518108)
Christine McCormack (3518111)
Fabrizio Gasparini (3011970)
Salah-Dine Chibout (370640)
Olivier Grenet (106357)
Jonathan Moggs (147210)
Baltazar Gomez-Mancilla (3518099)
Rémi Terranova (92125)

February 2016

Selected FMR1 genomic regions of methylation change throughout the FMR1 locus (Fig. 2a, Additional f...

Additional file 10: Table S3. of Reciprocal changes in DNA methylation and hydroxymethylation and a broad repressive epigenetic switch characterize FMR1 transcriptional silencing in fragile X syndrome

Sarah Brasa (226861)
Arne Mueller (3518105)
SĂŠbastien Jacquemont (3518102)
Florian Hahne (14246)
Izabela Rozenberg (214521)
Thomas Peters (147287)
Yunsheng He (3518108)
Christine McCormack (3518111)
Fabrizio Gasparini (3011970)
Salah-Dine Chibout (370640)
Olivier Grenet (106357)
Jonathan Moggs (147210)
Baltazar Gomez-Mancilla (3518099)
RĂŠmi Terranova (3518096)

February 2016

List of pyrosequencing assays. This table indicates the primers sequence as well as chromosome coord...

Additional file 1: of Incomplete silencing of full mutation alleles in males with fragile X syndrome is associated with autistic features

Emma Baker (5599862)
Marta Arpone (6665135)
Solange Aliaga (6665138)
Lesley Bretherton (779468)
Claudine Kraan (6665144)
Minh Bui (659178)
Howard Slater (6665150)
Ling Ling (268114)
David Francis (39274)
Matthew Hunter (362174)
Justine Elliott (6665159)
Carolyn Rogers (5599871)
Michael Field (245614)
Jonathan Cohen (26835)
Kim Cornish (5074844)
Lorena Santa Maria (6665165)
Victor Faundes (6665168)
Bianca Curotto (6665171)
Paulina Morales (6665174)
Cesar Trigo (6665177)
Isabel Salas (3827938)
Angelica Alliende (6665180)
David Amor (4877491)
David Godler (5599865)

May 2019

Table S1. Comparison between males and females intellectual functioning (standard) scores. Table S2....

Table_1_Targeted Reactivation of FMR1 Transcription in Fragile X Syndrome Embryonic Stem Cells.XLSX

Jill M. Haenfler (5632481)
Geena Skariah (4218448)
Caitlin M. Rodriguez (5632487)
Andre Monteiro da Rocha (5632490)
Jack M. Parent (358783)
Gary D. Smith (80822)
Peter K. Todd (235636)

August 2018

Fragile X Syndrome (FXS) is the most common inherited cause of intellectual disability and autism. I...

Reciprocal changes in DNA methylation and hydroxymethylation and a broad repressive epigenetic switch characterize FMR1 transcriptional silencing in Fragile X syndrome

Brasa, Sarah
Sebastien, Jacquemont
Hahne, Florian
Rozenberg, Izabela
Peters, Thomas
He, Yunsheng
Mccormack, Christine
Gasparini, Fabrizio
Chibout, Salah-Dine
Grenet, Olivier
Moggs, Jonathan
Gomez-Mancilla, Baltazar
Terranova, Remi

January 2016

Background. The molecular pathways associated with FMR1 epigenetic silencing in Fragile X syndrome (...

MOESM8 of Genome-wide methylation analysis demonstrates that 5-aza-2-deoxycytidine treatment does not cause random DNA demethylation in fragile X syndrome cells

Elisabetta Tabolacci (268801)
Giorgia Mancano (434928)
Stella Lanni (434925)
Federica Palumbo (3569810)
Martina Goracci (434926)
Fabrizio FerrĂ¨ (3459266)
Manuela Helmer-Citterich (10228)
Giovanni Neri (109017)

March 2016

Additional file 8: Table S5. List of DMRs and their chromosome position in the comparison between WT...

MOESM1 of Genome-wide methylation analysis demonstrates that 5-aza-2-deoxycytidine treatment does not cause random DNA demethylation in fragile X syndrome cells

Elisabetta Tabolacci (268801)
Giorgia Mancano (434928)
Stella Lanni (434925)
Federica Palumbo (3569810)
Martina Goracci (434926)
Fabrizio FerrĂ¨ (3459266)
Manuela Helmer-Citterich (10228)
Giovanni Neri (109017)

March 2016

Additional file 1: Figure S1. Bisulphite sequencing of the FMR1 methylation boundary after 5-azadC t...

Reciprocal changes in DNA methylation and hydroxymethylation and a broad repressive epigenetic switch characterize FMR1 transcriptional silencing in fragile X syndrome.

Brasa, S.
Mueller, A.
Jacquemont, S.
Hahne, F.
Rozenberg, I.
Peters, T.
He, Y.
McCormack, C.
Gasparini, F.
Chibout, S.D.
Grenet, O.
Moggs, J.
Gomez-Mancilla, B.
Terranova, R.

January 2016

BACKGROUND: Fragile X syndrome (FXS) is the most common form of inherited intellectual disability, r...

MOESM7 of Genome-wide methylation analysis demonstrates that 5-aza-2-deoxycytidine treatment does not cause random DNA demethylation in fragile X syndrome cells

Elisabetta Tabolacci (268801)
Giorgia Mancano (434928)
Stella Lanni (434925)
Federica Palumbo (3569810)
Martina Goracci (434926)
Fabrizio FerrĂ¨ (3459266)
Manuela Helmer-Citterich (10228)
Giovanni Neri (109017)

March 2016

Additional file 7: Table S4. List of DMRs and their chromosome position in the comparison between WT...

Reciprocal changes in DNA methylation and hydroxymethylation and a broad repressive epigenetic switch characterize FMR1 transcriptional silencing in fragile X syndrome.

Brasa, S.
Mueller, A.
Jacquemont, S.
Hahne, F.
Rozenberg, I.
Peters, T.
He, Y.
McCormack, C.
Gasparini, F.
Chibout, S.D.
Grenet, O.
Moggs, J.
Gomez-Mancilla, B.
Terranova, R.

January 2016

BACKGROUND: Fragile X syndrome (FXS) is the most common form of inherited intellectual disability, r...

Additional file 2: Table S1. of The developmental regulator PKL is required to maintain correct DNA methylation patterns at RNA-directed DNA methylation loci

Rong Yang (107028)
Zhimin Zheng (436481)
Qing Chen (131379)
Lan Yang (457660)
Huan Huang (724980)
Daisuke Miki (105782)
Wenwu Wu (196470)
Liang Zeng (791005)
Jun Liu (42548)
Jin-Xing Zhou (167426)
Joe Ogas (4058497)
Jian-Kang Zhu (23700)
Xin-Jian He (167435)
Heng Zhang (320479)

May 2017

Statistics of RNA-seq data. Table S2. List of differentially expressed genes in the pkl mutant ident...

Ahrim Youn (4606252)
Kyung In Kim (47502)
Raul Rabadan (88130)
Benjamin Tycko (237065)
Yufeng Shen (239573)
Shuang Wang (46453)

November 2018

Table S4. CDGs associated with significant genome-wide methylation changes in one cancer type. Hyper...

Additional file 9: Table S2. of Reciprocal changes in DNA methylation and hydroxymethylation and a broad repressive epigenetic switch characterize FMR1 transcriptional silencing in fragile X syndrome

Sarah Brasa (226861)
Arne Mueller (3518105)
SĂŠbastien Jacquemont (3518102)
Florian Hahne (14246)
Izabela Rozenberg (214521)
Thomas Peters (147287)
Yunsheng He (3518108)
Christine McCormack (3518111)
Fabrizio Gasparini (3011970)
Salah-Dine Chibout (370640)
Olivier Grenet (106357)
Jonathan Moggs (147210)
Baltazar Gomez-Mancilla (3518099)
RĂŠmi Terranova (3518096)

February 2016

List of the real-time qPCR assays. This table indicates the primers sequence as well as chromosome c...

Sarah Brasa (226861)
Arne Mueller (3518105)
Sébastien Jacquemont (3518123)
Florian Hahne (14246)
Izabela Rozenberg (214521)
Thomas Peters (147287)
Yunsheng He (3518108)
Christine McCormack (3518111)
Fabrizio Gasparini (3011970)
Salah-Dine Chibout (370640)
Olivier Grenet (106357)
Jonathan Moggs (147210)
Baltazar Gomez-Mancilla (3518099)
Rémi Terranova (92125)

February 2016

Selected FMR1 genomic regions of methylation change throughout the FMR1 locus (Fig. 2a, Additional f...

Sarah Brasa (226861)
Arne Mueller (3518105)
SĂŠbastien Jacquemont (3518102)
Florian Hahne (14246)
Izabela Rozenberg (214521)
Thomas Peters (147287)
Yunsheng He (3518108)
Christine McCormack (3518111)
Fabrizio Gasparini (3011970)
Salah-Dine Chibout (370640)
Olivier Grenet (106357)
Jonathan Moggs (147210)
Baltazar Gomez-Mancilla (3518099)
RĂŠmi Terranova (3518096)

February 2016

List of pyrosequencing assays. This table indicates the primers sequence as well as chromosome coord...

Additional file 1: of Incomplete silencing of full mutation alleles in males with fragile X syndrome is associated with autistic features

Emma Baker (5599862)
Marta Arpone (6665135)
Solange Aliaga (6665138)
Lesley Bretherton (779468)
Claudine Kraan (6665144)
Minh Bui (659178)
Howard Slater (6665150)
Ling Ling (268114)
David Francis (39274)
Matthew Hunter (362174)
Justine Elliott (6665159)
Carolyn Rogers (5599871)
Michael Field (245614)
Jonathan Cohen (26835)
Kim Cornish (5074844)
Lorena Santa Maria (6665165)
Victor Faundes (6665168)
Bianca Curotto (6665171)
Paulina Morales (6665174)
Cesar Trigo (6665177)
Isabel Salas (3827938)
Angelica Alliende (6665180)
David Amor (4877491)
David Godler (5599865)

May 2019

Table S1. Comparison between males and females intellectual functioning (standard) scores. Table S2....

Table_1_Targeted Reactivation of FMR1 Transcription in Fragile X Syndrome Embryonic Stem Cells.XLSX

Jill M. Haenfler (5632481)
Geena Skariah (4218448)
Caitlin M. Rodriguez (5632487)
Andre Monteiro da Rocha (5632490)
Jack M. Parent (358783)
Gary D. Smith (80822)
Peter K. Todd (235636)

August 2018

Fragile X Syndrome (FXS) is the most common inherited cause of intellectual disability and autism. I...

Reciprocal changes in DNA methylation and hydroxymethylation and a broad repressive epigenetic switch characterize FMR1 transcriptional silencing in Fragile X syndrome

Brasa, Sarah
Sebastien, Jacquemont
Hahne, Florian
Rozenberg, Izabela
Peters, Thomas
He, Yunsheng
Mccormack, Christine
Gasparini, Fabrizio
Chibout, Salah-Dine
Grenet, Olivier
Moggs, Jonathan
Gomez-Mancilla, Baltazar
Terranova, Remi

January 2016

Background. The molecular pathways associated with FMR1 epigenetic silencing in Fragile X syndrome (...

MOESM8 of Genome-wide methylation analysis demonstrates that 5-aza-2-deoxycytidine treatment does not cause random DNA demethylation in fragile X syndrome cells

Elisabetta Tabolacci (268801)
Giorgia Mancano (434928)
Stella Lanni (434925)
Federica Palumbo (3569810)
Martina Goracci (434926)
Fabrizio FerrĂ¨ (3459266)
Manuela Helmer-Citterich (10228)
Giovanni Neri (109017)

March 2016

Additional file 8: Table S5. List of DMRs and their chromosome position in the comparison between WT...

MOESM1 of Genome-wide methylation analysis demonstrates that 5-aza-2-deoxycytidine treatment does not cause random DNA demethylation in fragile X syndrome cells

Elisabetta Tabolacci (268801)
Giorgia Mancano (434928)
Stella Lanni (434925)
Federica Palumbo (3569810)
Martina Goracci (434926)
Fabrizio FerrĂ¨ (3459266)
Manuela Helmer-Citterich (10228)
Giovanni Neri (109017)

March 2016

Additional file 1: Figure S1. Bisulphite sequencing of the FMR1 methylation boundary after 5-azadC t...

Reciprocal changes in DNA methylation and hydroxymethylation and a broad repressive epigenetic switch characterize FMR1 transcriptional silencing in fragile X syndrome.

Brasa, S.
Mueller, A.
Jacquemont, S.
Hahne, F.
Rozenberg, I.
Peters, T.
He, Y.
McCormack, C.
Gasparini, F.
Chibout, S.D.
Grenet, O.
Moggs, J.
Gomez-Mancilla, B.
Terranova, R.

January 2016

BACKGROUND: Fragile X syndrome (FXS) is the most common form of inherited intellectual disability, r...

MOESM7 of Genome-wide methylation analysis demonstrates that 5-aza-2-deoxycytidine treatment does not cause random DNA demethylation in fragile X syndrome cells

Elisabetta Tabolacci (268801)
Giorgia Mancano (434928)
Stella Lanni (434925)
Federica Palumbo (3569810)
Martina Goracci (434926)
Fabrizio FerrĂ¨ (3459266)
Manuela Helmer-Citterich (10228)
Giovanni Neri (109017)

March 2016

Additional file 7: Table S4. List of DMRs and their chromosome position in the comparison between WT...

Reciprocal changes in DNA methylation and hydroxymethylation and a broad repressive epigenetic switch characterize FMR1 transcriptional silencing in fragile X syndrome.

Brasa, S.
Mueller, A.
Jacquemont, S.
Hahne, F.
Rozenberg, I.
Peters, T.
He, Y.
McCormack, C.
Gasparini, F.
Chibout, S.D.
Grenet, O.
Moggs, J.
Gomez-Mancilla, B.
Terranova, R.

January 2016

BACKGROUND: Fragile X syndrome (FXS) is the most common form of inherited intellectual disability, r...

Additional file 2: Table S1. of The developmental regulator PKL is required to maintain correct DNA methylation patterns at RNA-directed DNA methylation loci

Rong Yang (107028)
Zhimin Zheng (436481)
Qing Chen (131379)
Lan Yang (457660)
Huan Huang (724980)
Daisuke Miki (105782)
Wenwu Wu (196470)
Liang Zeng (791005)
Jun Liu (42548)
Jin-Xing Zhou (167426)
Joe Ogas (4058497)
Jian-Kang Zhu (23700)
Xin-Jian He (167435)
Heng Zhang (320479)

May 2017

Statistics of RNA-seq data. Table S2. List of differentially expressed genes in the pkl mutant ident...

Ahrim Youn (4606252)
Kyung In Kim (47502)
Raul Rabadan (88130)
Benjamin Tycko (237065)
Yufeng Shen (239573)
Shuang Wang (46453)

November 2018

Table S4. CDGs associated with significant genome-wide methylation changes in one cancer type. Hyper...

Additional file 6: Table S5. of Reciprocal changes in DNA methylation and hydroxymethylation and a broad repressive epigenetic switch characterize FMR1 transcriptional silencing in fragile X syndrome

Abstract

Extracted data

Additional file 6: Table S5. of Reciprocal changes in DNA methylation and hydroxymethylation and a broad repressive epigenetic switch characterize FMR1 transcriptional silencing in fragile X syndrome

Abstract

Extracted data

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