Additional file 1: of Intragenic sequences in the trophectoderm harbour the greatest proportion of methylation errors in day 17 bovine conceptuses generated using assisted reproductive technologies

Additional file 3: of DNA methylation patterns in peripheral blood mononuclear cells from Holstein cattle with variable milk yield

Chad Dechow (5849663)
Wan-Sheng Liu (200939)

October 2018

Table S3. Chromosome, start nucleotide, end nucleotide, length, summit, tags, Log P, and fold enrich...

Additional file 4: of DNA methylation patterns in peripheral blood mononuclear cells from Holstein cattle with variable milk yield

Chad Dechow (5849663)
Wan-Sheng Liu (200939)

October 2018

Table S4. Chromosome, start nucleotide, end nucleotide, length, summit, tags, Log P, and fold enrich...

Additional file 5: of DNA methylation patterns in peripheral blood mononuclear cells from Holstein cattle with variable milk yield

Chad Dechow (5849663)
Wan-Sheng Liu (200939)

October 2018

Table S5. Chromosome, start nucleotide, end nucleotide, length, summit, tags, Log P, and fold enrich...

Additional file 2: of Intragenic sequences in the trophectoderm harbour the greatest proportion of methylation errors in day 17 bovine conceptuses generated using assisted reproductive technologies

Alan OâDoherty (5338046)
Paul McGettigan (739859)
Rachelle Irwin (3477233)
David Magee (3409391)
Dominic Gagne (5338043)
Eric Fournier (502444)
Abdullah Al-Naib (5338049)
Marc-AndrĂŠ Sirard (3465899)
Colum Walsh (3477236)
Claude Robert (255405)
Trudee Fair (476830)

June 2018

Comparison of differentially methylated genes with previously published imprinted genes. (XLS 28 kb

Additional file 4: of Intragenic sequences in the trophectoderm harbour the greatest proportion of methylation errors in day 17 bovine conceptuses generated using assisted reproductive technologies

Alan OâDoherty (5338046)
Paul McGettigan (739859)
Rachelle Irwin (3477233)
David Magee (3409391)
Dominic Gagne (5338043)
Eric Fournier (502444)
Abdullah Al-Naib (5338049)
Marc-AndrĂŠ Sirard (3465899)
Colum Walsh (3477236)
Claude Robert (255405)
Trudee Fair (476830)

June 2018

Quality control plots for all samples generated after EDMA microarray hybridization and data analysi...

Additional file 5: of Intragenic sequences in the trophectoderm harbour the greatest proportion of methylation errors in day 17 bovine conceptuses generated using assisted reproductive technologies

Alan OâDoherty (5338046)
Paul McGettigan (739859)
Rachelle Irwin (3477233)
David Magee (3409391)
Dominic Gagne (5338043)
Eric Fournier (502444)
Abdullah Al-Naib (5338049)
Marc-AndrĂŠ Sirard (3465899)
Colum Walsh (3477236)
Claude Robert (255405)
Trudee Fair (476830)

June 2018

Table S1. Pyrosequencing primers used for array validation. Table S2. Primers used for gene expressi...

Additional file 3: of Genome-wide DNA methylation patterns of bovine blastocysts derived from in vivo embryos subjected to in vitro culture before, during or after embryonic genome activation

Dessie Salilew-Wondim (479277)
Mohammed Saeed-Zidane (822214)
Michael Hoelker (479275)
Samuel Gebremedhn (626335)
MikhaĂŤl Poirier (5331455)
Hari Pandey (5331452)
Ernst Tholen (79379)
Christiane Neuhoff (412997)
Eva Held (4126951)
Urban Besenfelder (822215)
Vita Havlicek (822216)
Franca Rings (79377)
Eric Fournier (502444)
Dominic GagnĂŠ (5331449)
Marc-AndrĂŠ Sirard (3465899)
Claude Robert (255405)
Ahmed Gad (412999)
Karl Schellander (79383)
Dawit Tesfaye (79384)

June 2018

Figure S1. The order of chromosomes based their probe density and differentially methylated probes (...

Additional file 1: of Genome-wide DNA methylation patterns of bovine blastocysts derived from in vivo embryos subjected to in vitro culture before, during or after embryonic genome activation

Dessie Salilew-Wondim (479277)
Mohammed Saeed-Zidane (822214)
Michael Hoelker (479275)
Samuel Gebremedhn (626335)
MikhaĂŤl Poirier (5331455)
Hari Pandey (5331452)
Ernst Tholen (79379)
Christiane Neuhoff (412997)
Eva Held (4126951)
Urban Besenfelder (822215)
Vita Havlicek (822216)
Franca Rings (79377)
Eric Fournier (502444)
Dominic GagnĂŠ (5331449)
Marc-AndrĂŠ Sirard (3465899)
Claude Robert (255405)
Ahmed Gad (412999)
Karl Schellander (79383)
Dawit Tesfaye (79384)

June 2018

Table S1. The list of primers used to validate DMRs in blastocysts of different groups using bisulfi...

Additional file 9: of DNA methylation patterns in peripheral blood mononuclear cells from Holstein cattle with variable milk yield

Chad Dechow (5849663)
Wan-Sheng Liu (200939)

October 2018

Table S8. Location (chromosome, starting and ending nucleotide) of putative case-control differentia...

Additional file 2: of Genome-wide DNA methylation patterns of bovine blastocysts derived from in vivo embryos subjected to in vitro culture before, during or after embryonic genome activation

Dessie Salilew-Wondim (479277)
Mohammed Saeed-Zidane (822214)
Michael Hoelker (479275)
Samuel Gebremedhn (626335)
MikhaĂŤl Poirier (5331455)
Hari Pandey (5331452)
Ernst Tholen (79379)
Christiane Neuhoff (412997)
Eva Held (4126951)
Urban Besenfelder (822215)
Vita Havlicek (822216)
Franca Rings (79377)
Eric Fournier (502444)
Dominic GagnĂŠ (5331449)
Marc-AndrĂŠ Sirard (3465899)
Claude Robert (255405)
Ahmed Gad (412999)
Karl Schellander (79383)
Dawit Tesfaye (79384)

June 2018

Table S2. The list of primers used for validation of the differentially expressed genes using qPCR. ...

Intragenic sequences in the trophectoderm harbour the greatest proportion of methylation errors in day 17 bovine conceptuses generated using assisted reproductive technologies

O'Doherty, Alan M.
McGettigan, Paul A.
Irwin, Rachelle E.
Magee, David A.
Fair, Trudee
et al.

June 2019

Background: Assisted reproductive technologies (ART) are widely used to treat fertility issues in hu...

Additional file 10: of DNA methylation patterns in peripheral blood mononuclear cells from Holstein cattle with variable milk yield

Chad Dechow (5849663)
Wan-Sheng Liu (200939)

October 2018

Table S9. Location (chromosome, starting and ending nucleotide) of putative environmental differenti...

Additional file 4: of Genome-wide DNA methylation patterns of bovine blastocysts derived from in vivo embryos subjected to in vitro culture before, during or after embryonic genome activation

Dessie Salilew-Wondim (479277)
Mohammed Saeed-Zidane (822214)
Michael Hoelker (479275)
Samuel Gebremedhn (626335)
MikhaĂŤl Poirier (5331455)
Hari Pandey (5331452)
Ernst Tholen (79379)
Christiane Neuhoff (412997)
Eva Held (4126951)
Urban Besenfelder (822215)
Vita Havlicek (822216)
Franca Rings (79377)
Eric Fournier (502444)
Dominic GagnĂŠ (5331449)
Marc-AndrĂŠ Sirard (3465899)
Claude Robert (255405)
Ahmed Gad (412999)
Karl Schellander (79383)
Dawit Tesfaye (79384)

June 2018

Figure S2. The circos plot representing the overall methylation levels in the in different blastocys...

Additional file 1: of DNA methylation patterns in peripheral blood mononuclear cells from Holstein cattle with variable milk yield

Chad Dechow (5849663)
Wan-Sheng Liu (200939)

October 2018

Table S1. Chromosome, start nucleotide, end nucleotide, length, summit, tags, Log P, and fold enrich...

Additional file 6: of DNA methylation patterns in peripheral blood mononuclear cells from Holstein cattle with variable milk yield

Chad Dechow (5849663)
Wan-Sheng Liu (200939)

October 2018

Table S6. Chromosome, start nucleotide, end nucleotide, length, summit, tags, Log P, and fold enrich...

Additional file 3: of DNA methylation patterns in peripheral blood mononuclear cells from Holstein cattle with variable milk yield

Chad Dechow (5849663)
Wan-Sheng Liu (200939)

October 2018

Table S3. Chromosome, start nucleotide, end nucleotide, length, summit, tags, Log P, and fold enrich...

Additional file 4: of DNA methylation patterns in peripheral blood mononuclear cells from Holstein cattle with variable milk yield

Chad Dechow (5849663)
Wan-Sheng Liu (200939)

October 2018

Table S4. Chromosome, start nucleotide, end nucleotide, length, summit, tags, Log P, and fold enrich...

Additional file 5: of DNA methylation patterns in peripheral blood mononuclear cells from Holstein cattle with variable milk yield

Chad Dechow (5849663)
Wan-Sheng Liu (200939)

October 2018

Table S5. Chromosome, start nucleotide, end nucleotide, length, summit, tags, Log P, and fold enrich...

Additional file 2: of Intragenic sequences in the trophectoderm harbour the greatest proportion of methylation errors in day 17 bovine conceptuses generated using assisted reproductive technologies

Alan OâDoherty (5338046)
Paul McGettigan (739859)
Rachelle Irwin (3477233)
David Magee (3409391)
Dominic Gagne (5338043)
Eric Fournier (502444)
Abdullah Al-Naib (5338049)
Marc-AndrĂŠ Sirard (3465899)
Colum Walsh (3477236)
Claude Robert (255405)
Trudee Fair (476830)

June 2018

Comparison of differentially methylated genes with previously published imprinted genes. (XLS 28 kb

Additional file 4: of Intragenic sequences in the trophectoderm harbour the greatest proportion of methylation errors in day 17 bovine conceptuses generated using assisted reproductive technologies

Alan OâDoherty (5338046)
Paul McGettigan (739859)
Rachelle Irwin (3477233)
David Magee (3409391)
Dominic Gagne (5338043)
Eric Fournier (502444)
Abdullah Al-Naib (5338049)
Marc-AndrĂŠ Sirard (3465899)
Colum Walsh (3477236)
Claude Robert (255405)
Trudee Fair (476830)

June 2018

Quality control plots for all samples generated after EDMA microarray hybridization and data analysi...

Additional file 5: of Intragenic sequences in the trophectoderm harbour the greatest proportion of methylation errors in day 17 bovine conceptuses generated using assisted reproductive technologies

Alan OâDoherty (5338046)
Paul McGettigan (739859)
Rachelle Irwin (3477233)
David Magee (3409391)
Dominic Gagne (5338043)
Eric Fournier (502444)
Abdullah Al-Naib (5338049)
Marc-AndrĂŠ Sirard (3465899)
Colum Walsh (3477236)
Claude Robert (255405)
Trudee Fair (476830)

June 2018

Table S1. Pyrosequencing primers used for array validation. Table S2. Primers used for gene expressi...

Additional file 3: of Genome-wide DNA methylation patterns of bovine blastocysts derived from in vivo embryos subjected to in vitro culture before, during or after embryonic genome activation

Dessie Salilew-Wondim (479277)
Mohammed Saeed-Zidane (822214)
Michael Hoelker (479275)
Samuel Gebremedhn (626335)
MikhaĂŤl Poirier (5331455)
Hari Pandey (5331452)
Ernst Tholen (79379)
Christiane Neuhoff (412997)
Eva Held (4126951)
Urban Besenfelder (822215)
Vita Havlicek (822216)
Franca Rings (79377)
Eric Fournier (502444)
Dominic GagnĂŠ (5331449)
Marc-AndrĂŠ Sirard (3465899)
Claude Robert (255405)
Ahmed Gad (412999)
Karl Schellander (79383)
Dawit Tesfaye (79384)

June 2018

Figure S1. The order of chromosomes based their probe density and differentially methylated probes (...

Additional file 1: of Genome-wide DNA methylation patterns of bovine blastocysts derived from in vivo embryos subjected to in vitro culture before, during or after embryonic genome activation

Dessie Salilew-Wondim (479277)
Mohammed Saeed-Zidane (822214)
Michael Hoelker (479275)
Samuel Gebremedhn (626335)
MikhaĂŤl Poirier (5331455)
Hari Pandey (5331452)
Ernst Tholen (79379)
Christiane Neuhoff (412997)
Eva Held (4126951)
Urban Besenfelder (822215)
Vita Havlicek (822216)
Franca Rings (79377)
Eric Fournier (502444)
Dominic GagnĂŠ (5331449)
Marc-AndrĂŠ Sirard (3465899)
Claude Robert (255405)
Ahmed Gad (412999)
Karl Schellander (79383)
Dawit Tesfaye (79384)

June 2018

Table S1. The list of primers used to validate DMRs in blastocysts of different groups using bisulfi...

Additional file 9: of DNA methylation patterns in peripheral blood mononuclear cells from Holstein cattle with variable milk yield

Chad Dechow (5849663)
Wan-Sheng Liu (200939)

October 2018

Table S8. Location (chromosome, starting and ending nucleotide) of putative case-control differentia...

Additional file 2: of Genome-wide DNA methylation patterns of bovine blastocysts derived from in vivo embryos subjected to in vitro culture before, during or after embryonic genome activation

Dessie Salilew-Wondim (479277)
Mohammed Saeed-Zidane (822214)
Michael Hoelker (479275)
Samuel Gebremedhn (626335)
MikhaĂŤl Poirier (5331455)
Hari Pandey (5331452)
Ernst Tholen (79379)
Christiane Neuhoff (412997)
Eva Held (4126951)
Urban Besenfelder (822215)
Vita Havlicek (822216)
Franca Rings (79377)
Eric Fournier (502444)
Dominic GagnĂŠ (5331449)
Marc-AndrĂŠ Sirard (3465899)
Claude Robert (255405)
Ahmed Gad (412999)
Karl Schellander (79383)
Dawit Tesfaye (79384)

June 2018

Table S2. The list of primers used for validation of the differentially expressed genes using qPCR. ...

Intragenic sequences in the trophectoderm harbour the greatest proportion of methylation errors in day 17 bovine conceptuses generated using assisted reproductive technologies

O'Doherty, Alan M.
McGettigan, Paul A.
Irwin, Rachelle E.
Magee, David A.
Fair, Trudee
et al.

June 2019

Background: Assisted reproductive technologies (ART) are widely used to treat fertility issues in hu...

Additional file 10: of DNA methylation patterns in peripheral blood mononuclear cells from Holstein cattle with variable milk yield

Chad Dechow (5849663)
Wan-Sheng Liu (200939)

October 2018

Table S9. Location (chromosome, starting and ending nucleotide) of putative environmental differenti...

Additional file 4: of Genome-wide DNA methylation patterns of bovine blastocysts derived from in vivo embryos subjected to in vitro culture before, during or after embryonic genome activation

Dessie Salilew-Wondim (479277)
Mohammed Saeed-Zidane (822214)
Michael Hoelker (479275)
Samuel Gebremedhn (626335)
MikhaĂŤl Poirier (5331455)
Hari Pandey (5331452)
Ernst Tholen (79379)
Christiane Neuhoff (412997)
Eva Held (4126951)
Urban Besenfelder (822215)
Vita Havlicek (822216)
Franca Rings (79377)
Eric Fournier (502444)
Dominic GagnĂŠ (5331449)
Marc-AndrĂŠ Sirard (3465899)
Claude Robert (255405)
Ahmed Gad (412999)
Karl Schellander (79383)
Dawit Tesfaye (79384)

June 2018

Figure S2. The circos plot representing the overall methylation levels in the in different blastocys...

Additional file 1: of DNA methylation patterns in peripheral blood mononuclear cells from Holstein cattle with variable milk yield

Chad Dechow (5849663)
Wan-Sheng Liu (200939)

October 2018

Table S1. Chromosome, start nucleotide, end nucleotide, length, summit, tags, Log P, and fold enrich...

Additional file 6: of DNA methylation patterns in peripheral blood mononuclear cells from Holstein cattle with variable milk yield

Chad Dechow (5849663)
Wan-Sheng Liu (200939)

October 2018

Table S6. Chromosome, start nucleotide, end nucleotide, length, summit, tags, Log P, and fold enrich...

Additional file 3: of DNA methylation patterns in peripheral blood mononuclear cells from Holstein cattle with variable milk yield

Chad Dechow (5849663)
Wan-Sheng Liu (200939)

October 2018

Table S3. Chromosome, start nucleotide, end nucleotide, length, summit, tags, Log P, and fold enrich...

Additional file 4: of DNA methylation patterns in peripheral blood mononuclear cells from Holstein cattle with variable milk yield

Chad Dechow (5849663)
Wan-Sheng Liu (200939)

October 2018

Table S4. Chromosome, start nucleotide, end nucleotide, length, summit, tags, Log P, and fold enrich...

Additional file 5: of DNA methylation patterns in peripheral blood mononuclear cells from Holstein cattle with variable milk yield

Chad Dechow (5849663)
Wan-Sheng Liu (200939)

October 2018

Table S5. Chromosome, start nucleotide, end nucleotide, length, summit, tags, Log P, and fold enrich...

Additional file 1: of Intragenic sequences in the trophectoderm harbour the greatest proportion of methylation errors in day 17 bovine conceptuses generated using assisted reproductive technologies

Abstract

Extracted data

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