Additional file 6: Figure S5. of Full-length autonomous transposable elements are preferentially targeted by expression-dependent forms of RNA-directed DNA methylation

Kaushik Panda (3434813)
Lexiang Ji (615409)
Drexel Neumann (3434810)
Josquin Daron (3434801)
Robert Schmitz (3434804)
R. Slotkin (3434807)

Publication date

August 2016

DOI

10.6084/m9.figshare.c.3604448_d9.v1

Abstract

Genome-wide distribution of TE CG and CHG methylation. Heatmap showing CG and CHG methylation for the TEs categorized into different RdDM mechanisms based on CHH methylation. (PDF 394 kb

Extracted data

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Additional file 6: Figure S5. of Full-length autonomous transposable elements are preferentially targeted by expression-dependent forms of RNA-directed DNA methylation

Kaushik Panda (3434813)
Lexiang Ji (615409)
Drexel Neumann (3434810)
Josquin Daron (3434801)
Robert Schmitz (3434804)
R. Slotkin (3434807)

Open link

Publication date

August 2016

DOI

10.6084/m9.figshare.c.3604448_d9.v1

Abstract

Genome-wide distribution of TE CG and CHG methylation. Heatmap showing CG and CHG methylation for the TEs categorized into different RdDM mechanisms based on CHH methylation. (PDF 394 kb

Extracted data

Topics

PDFMusic genre

Heatmap

Wataru Habano (3532949)
Kohei Kawamura (3532958)
Natsuki Iizuka (3532955)
Jun Terashima (3532952)
Tamotsu Sugai (144544)
Shogo Ozawa (775524)

September 2015

DNA methylation mapping of BMP4 and IGFBP3 tumor suppressor genes in the three hepatoma cell lines. ...

Average CHH methylation levels in transposable elements (TEs) (A) and genes (B).

Chao-Feng Huang (457657)
Daisuke Miki (105782)
Kai Tang (138245)
Hao-Ran Zhou (457658)
Zhimin Zheng (436481)
Wei Chen (23863)
Ze-Yang Ma (457659)
Lan Yang (457660)
Heng Zhang (320479)
Renyi Liu (92885)
Xin-Jian He (167435)
Jian-Kang Zhu (23700)

September 2013

TEs and genes were divided into 5 groups based on their size for detailed comparison of the DNA m...

Additional file 5: Figure S4. of Full-length autonomous transposable elements are preferentially targeted by expression-dependent forms of RNA-directed DNA methylation

Kaushik Panda (3434813)
Lexiang Ji (615409)
Drexel Neumann (3434810)
Josquin Daron (3434801)
Robert Schmitz (3434804)
R. Slotkin (3434807)

August 2016

Overlap in DMRs and TEs regulated by RdDM. Comparison of the relative efficacy of RdDM mechanisms in...

Additional file 2: of Full-length autonomous transposable elements are preferentially targeted by expression-dependent forms of RNA-directed DNA methylation

Kaushik Panda (3434813)
Lexiang Ji (615409)
Drexel Neumann (3434810)
Josquin Daron (3434801)
Robert Schmitz (3434804)
R. Slotkin (3434807)

August 2016

Results and Methods. Detailed Results, Methods, Figure Legends, and References to support the Supple...

Additional file 4: Figure S3. of Full-length autonomous transposable elements are preferentially targeted by expression-dependent forms of RNA-directed DNA methylation

Kaushik Panda (3434813)
Lexiang Ji (615409)
Drexel Neumann (3434810)
Josquin Daron (3434801)
Robert Schmitz (3434804)
R. Slotkin (3434807)

August 2016

Validation of MethylC-seq data using biological replicates of key genotypes. Analyses of biological ...

Additional file 11: Table S1. of Full-length autonomous transposable elements are preferentially targeted by expression-dependent forms of RNA-directed DNA methylation

Kaushik Panda (3434813)
Lexiang Ji (615409)
Drexel Neumann (3434810)
Josquin Daron (3434801)
Robert Schmitz (3434804)
R. Slotkin (3434807)

August 2016

Mutant alleles and quality statistics of the MethylC-seq data produced in this study. Reads from our...

Additional file 12: Table S2. of Full-length autonomous transposable elements are preferentially targeted by expression-dependent forms of RNA-directed DNA methylation

Kaushik Panda (3434813)
Lexiang Ji (615409)
Drexel Neumann (3434810)
Josquin Daron (3434801)
Robert Schmitz (3434804)
R. Slotkin (3434807)

August 2016

Primer sequences used in this report. Primer sequences for single-locus bisulfite sequencing perform...

Additional file 20: of Maize RNA PolIV affects the expression of genes with nearby TE insertions and has a genome-wide repressive impact on transcription

Cristian Forestan (4511065)
Silvia Farinati (2058778)
Riccardo Aiese Cigliano (4511068)
Alice Lunardon (4511059)
Walter Sanseverino (3498791)
Serena Varotto (4511062)

October 2017

DNA methylation profiles at differentially expressed gene flanking regions. Methylation levels in ea...

Additional file 7: of Functional variation in allelic methylomes underscores a strong genetic contribution and reveals novel epigenetic alterations in the human epigenome

Warren Cheung (83908)
Xiaojian Shao (3465695)
Andréanne Morin (3499337)
Valérie Siroux (271568)
Tony Kwan (232656)
Bing Ge (42609)
Dylan Aïssi (635733)
Lu Chen (75170)
Louella Vasquez (3830902)
Fiona Allum (3465704)
Frédéric Guénard (684715)
Emmanuelle Bouzigon (166245)
Marie-Michelle Simon (3465701)
Elodie Boulier (3830896)
Adriana Redensek (3830905)
Stephen Watt (377395)
Avik Datta (3830908)
Laura Clarke (2190)
Paul Flicek (77154)
Daniel Mead (3507788)
Dirk Paul (3428945)
Stephan Beck (5246)
Guillaume Bourque (123960)
Mark Lathrop (17971)
André Tchernof (541752)
Marie-Claude Vohl (684717)
Florence Demenais (73668)
Isabelle Pin (166259)
Kate Downes (242215)
Hendrick Stunnenberg (3830899)
Nicole Soranzo (12361)
Tomi Pastinen (15737)
Elin Grundberg (116416)

March 2017

Allelic methylation in enhancer peaks. In this file, we report the ChromHMM bin and the allele-sepci...

Additional file 1: Figure 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

RDM18/PKL promotes silencing at the p35S-NPTII transgene but does not affect DNA methylation levels....

Additional file 4: of Integrated analyses of multi-omics reveal global patterns of methylation and hydroxymethylation and screen the tumor suppressive roles of HADHB in colorectal cancer

Yimin Zhu (101874)
Hanlin Lu (2925378)
Dandan Zhang (228849)
Meiyan Li (441468)
Xiaohui Sun (520181)
Ledong Wan (1947580)
Dan Yu (214174)
Yiping Tian (4908259)
Hongchuan Jin (194460)
Aifen Lin (3504350)
Fei Gao (29262)
Maode Lai (15338)

March 2018

Figure S3. Methylation and hydroxymethylation levels distribution in different types of genomic elem...

A combined heat map shows the differential methylation of the 5,423 matched CpGs in conjunction with gene and CGI context for EIUM and OSIS.

Matthew T. Dyson (531983)
Damian Roqueiro (187645)
Diana Monsivais (187659)
C. Mutlu Ercan (531984)
Mary Ellen Pavone (531985)
David C. Brooks (531986)
Toshiyuki Kakinuma (324003)
Masanori Ono (249913)
Nadereh Jafari (138410)
Yang Dai (36730)
Serdar E. Bulun (187675)

March 2014

Relative DNA methylation from each subject is encoded for each CpG from unmethylated (β-value = 0...

Total number of differentially methylated cytosines (DMC) captured by epiGBS-R (reference branch) and WGBS in the three sequence contexts (CpG, CHG and CHH) in each genomic feature (promoter, down-stream of transcriptional sites, gene body and intergenic region), within transposable elements (TE) or outside (no TE) also indicated.

A. Niloya Troyee (16954564)
Cristian Peña-Ponton (16954567)
Mónica Medrano (437606)
Koen J. F. Verhoeven (12533266)
Conchita Alonso (3294657)

September 2023

Total number of differentially methylated cytosines (DMC) captured by epiGBS-R (reference branch) an...

Additional file 6: Figure S6. of Analysis of DNA methylation landscape reveals the roles of DNA methylation in the regulation of drug metabolizing enzymes

Wataru Habano (3532949)
Kohei Kawamura (3532958)
Natsuki Iizuka (3532955)
Jun Terashima (3532952)
Tamotsu Sugai (144544)
Shogo Ozawa (775524)

September 2015

DNA methylation mapping of BMP4 and IGFBP3 tumor suppressor genes in the three hepatoma cell lines. ...

Average CHH methylation levels in transposable elements (TEs) (A) and genes (B).

Chao-Feng Huang (457657)
Daisuke Miki (105782)
Kai Tang (138245)
Hao-Ran Zhou (457658)
Zhimin Zheng (436481)
Wei Chen (23863)
Ze-Yang Ma (457659)
Lan Yang (457660)
Heng Zhang (320479)
Renyi Liu (92885)
Xin-Jian He (167435)
Jian-Kang Zhu (23700)

September 2013

TEs and genes were divided into 5 groups based on their size for detailed comparison of the DNA m...

Additional file 5: Figure S4. of Full-length autonomous transposable elements are preferentially targeted by expression-dependent forms of RNA-directed DNA methylation

Kaushik Panda (3434813)
Lexiang Ji (615409)
Drexel Neumann (3434810)
Josquin Daron (3434801)
Robert Schmitz (3434804)
R. Slotkin (3434807)

August 2016

Overlap in DMRs and TEs regulated by RdDM. Comparison of the relative efficacy of RdDM mechanisms in...

Additional file 2: of Full-length autonomous transposable elements are preferentially targeted by expression-dependent forms of RNA-directed DNA methylation

Kaushik Panda (3434813)
Lexiang Ji (615409)
Drexel Neumann (3434810)
Josquin Daron (3434801)
Robert Schmitz (3434804)
R. Slotkin (3434807)

August 2016

Results and Methods. Detailed Results, Methods, Figure Legends, and References to support the Supple...

Additional file 4: Figure S3. of Full-length autonomous transposable elements are preferentially targeted by expression-dependent forms of RNA-directed DNA methylation

Kaushik Panda (3434813)
Lexiang Ji (615409)
Drexel Neumann (3434810)
Josquin Daron (3434801)
Robert Schmitz (3434804)
R. Slotkin (3434807)

August 2016

Validation of MethylC-seq data using biological replicates of key genotypes. Analyses of biological ...

Additional file 11: Table S1. of Full-length autonomous transposable elements are preferentially targeted by expression-dependent forms of RNA-directed DNA methylation

Kaushik Panda (3434813)
Lexiang Ji (615409)
Drexel Neumann (3434810)
Josquin Daron (3434801)
Robert Schmitz (3434804)
R. Slotkin (3434807)

August 2016

Mutant alleles and quality statistics of the MethylC-seq data produced in this study. Reads from our...

Additional file 12: Table S2. of Full-length autonomous transposable elements are preferentially targeted by expression-dependent forms of RNA-directed DNA methylation

Kaushik Panda (3434813)
Lexiang Ji (615409)
Drexel Neumann (3434810)
Josquin Daron (3434801)
Robert Schmitz (3434804)
R. Slotkin (3434807)

August 2016

Primer sequences used in this report. Primer sequences for single-locus bisulfite sequencing perform...

Additional file 20: of Maize RNA PolIV affects the expression of genes with nearby TE insertions and has a genome-wide repressive impact on transcription

Cristian Forestan (4511065)
Silvia Farinati (2058778)
Riccardo Aiese Cigliano (4511068)
Alice Lunardon (4511059)
Walter Sanseverino (3498791)
Serena Varotto (4511062)

October 2017

DNA methylation profiles at differentially expressed gene flanking regions. Methylation levels in ea...

Additional file 7: of Functional variation in allelic methylomes underscores a strong genetic contribution and reveals novel epigenetic alterations in the human epigenome

Warren Cheung (83908)
Xiaojian Shao (3465695)
Andréanne Morin (3499337)
Valérie Siroux (271568)
Tony Kwan (232656)
Bing Ge (42609)
Dylan Aïssi (635733)
Lu Chen (75170)
Louella Vasquez (3830902)
Fiona Allum (3465704)
Frédéric Guénard (684715)
Emmanuelle Bouzigon (166245)
Marie-Michelle Simon (3465701)
Elodie Boulier (3830896)
Adriana Redensek (3830905)
Stephen Watt (377395)
Avik Datta (3830908)
Laura Clarke (2190)
Paul Flicek (77154)
Daniel Mead (3507788)
Dirk Paul (3428945)
Stephan Beck (5246)
Guillaume Bourque (123960)
Mark Lathrop (17971)
André Tchernof (541752)
Marie-Claude Vohl (684717)
Florence Demenais (73668)
Isabelle Pin (166259)
Kate Downes (242215)
Hendrick Stunnenberg (3830899)
Nicole Soranzo (12361)
Tomi Pastinen (15737)
Elin Grundberg (116416)

March 2017

Allelic methylation in enhancer peaks. In this file, we report the ChromHMM bin and the allele-sepci...

Additional file 1: Figure 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

RDM18/PKL promotes silencing at the p35S-NPTII transgene but does not affect DNA methylation levels....

Additional file 4: of Integrated analyses of multi-omics reveal global patterns of methylation and hydroxymethylation and screen the tumor suppressive roles of HADHB in colorectal cancer

Yimin Zhu (101874)
Hanlin Lu (2925378)
Dandan Zhang (228849)
Meiyan Li (441468)
Xiaohui Sun (520181)
Ledong Wan (1947580)
Dan Yu (214174)
Yiping Tian (4908259)
Hongchuan Jin (194460)
Aifen Lin (3504350)
Fei Gao (29262)
Maode Lai (15338)

March 2018

Figure S3. Methylation and hydroxymethylation levels distribution in different types of genomic elem...

A combined heat map shows the differential methylation of the 5,423 matched CpGs in conjunction with gene and CGI context for EIUM and OSIS.

Matthew T. Dyson (531983)
Damian Roqueiro (187645)
Diana Monsivais (187659)
C. Mutlu Ercan (531984)
Mary Ellen Pavone (531985)
David C. Brooks (531986)
Toshiyuki Kakinuma (324003)
Masanori Ono (249913)
Nadereh Jafari (138410)
Yang Dai (36730)
Serdar E. Bulun (187675)

March 2014

Relative DNA methylation from each subject is encoded for each CpG from unmethylated (β-value = 0...

A. Niloya Troyee (16954564)
Cristian Peña-Ponton (16954567)
Mónica Medrano (437606)
Koen J. F. Verhoeven (12533266)
Conchita Alonso (3294657)

September 2023

Total number of differentially methylated cytosines (DMC) captured by epiGBS-R (reference branch) an...

Additional file 6: Figure S6. of Analysis of DNA methylation landscape reveals the roles of DNA methylation in the regulation of drug metabolizing enzymes

Wataru Habano (3532949)
Kohei Kawamura (3532958)
Natsuki Iizuka (3532955)
Jun Terashima (3532952)
Tamotsu Sugai (144544)
Shogo Ozawa (775524)

September 2015

DNA methylation mapping of BMP4 and IGFBP3 tumor suppressor genes in the three hepatoma cell lines. ...

Average CHH methylation levels in transposable elements (TEs) (A) and genes (B).

Chao-Feng Huang (457657)
Daisuke Miki (105782)
Kai Tang (138245)
Hao-Ran Zhou (457658)
Zhimin Zheng (436481)
Wei Chen (23863)
Ze-Yang Ma (457659)
Lan Yang (457660)
Heng Zhang (320479)
Renyi Liu (92885)
Xin-Jian He (167435)
Jian-Kang Zhu (23700)

September 2013

TEs and genes were divided into 5 groups based on their size for detailed comparison of the DNA m...

Additional file 6: Figure S5. of Full-length autonomous transposable elements are preferentially targeted by expression-dependent forms of RNA-directed DNA methylation

Abstract

Extracted data

Additional file 6: Figure S5. of Full-length autonomous transposable elements are preferentially targeted by expression-dependent forms of RNA-directed DNA methylation

Abstract

Extracted data

Topics

Related items

Topics

Related items