Additional file 9: Table S8. of Epigenetic modification with trichostatin A does not correct specific errors of somatic cell nuclear transfer at the transcriptomic level; highlighting the non-random nature of oocyte-mediated reprogramming errors

Additional file 1: of Incomplete cellular reprogramming of colorectal cancer cells elicits an epithelial/mesenchymal hybrid phenotype

Michele Hiew (5538686)
Han Cheng (475615)
Chiu-Jung Huang (3819067)
Kowit Chong (5538683)
Soon Cheong (3819064)
Kong Choo (3819061)
Tunku Kamarul (618729)

July 2018

Table S1. Primer sequences of genes and miRNAs analyzed in RT-PCR or qRT-PCR. (PDF 99 kb

Additional file 1: of The epigenetic regulation of HsMar1, a human DNA transposon

Sylvaine Renault (261575)
Murielle Genty (311750)
Alison Gabori (6339800)
Catherine Boisneau (6339803)
Charles Esnault (2386333)
Thomas DugĂŠ de Bernonville (6339806)
Corinne AugĂŠ-Gouillou (6339809)

February 2019

Data S1. Recombinant HsMar1 insertion sites in HeLa and CHO cell lines. Data S2. Inter-plasmidic act...

Additional file 3: of Transcriptional defects and reprogramming barriers in somatic cell nuclear reprogramming as revealed by single-embryo RNA sequencing

Yong Liu (6908)
Fengrui Wu (5639615)
Ling Zhang (18071)
Xiaoqing Wu (788978)
Dengkun Li (5639618)
Jing Xin (183453)
Juan Xie (461923)
Feng Kong (459884)
Wenying Wang (187565)
Qiaoqin Wu (5846117)
Di Zhang (197959)
Rong Wang (59795)
Shaorong Gao (249898)
Wenyong Li (715719)

October 2018

List of different genes between NT groups and Invivo group. Two group Ensembl gene IDs were listed. ...

Additional file 1: Table S1. of Epigenetic modification with trichostatin A does not correct specific errors of somatic cell nuclear transfer at the transcriptomic level; highlighting the non-random nature of oocyte-mediated reprogramming errors

Sayyed Hosseini (3465875)
Isabelle Dufort (3465890)
Julie Nieminen (3465872)
Fariba Moulavi (2587045)
Hamid Ghanaei (3465896)
Mahdi Hajian (3465884)
Farnoosh Jafarpour (3465881)
Mohsen Forouzanfar (3465893)
Hamid Gourbai (3465869)
Abdol Shahverdi (3465887)
Mohammad Nasr-Esfahani (3465878)
Marc-AndrĂŠ Sirard (3465899)

January 2016

Pre- and post- implantation development. Effect of TSA treatment on in vitro and in vivo development...

Additional file 6: Table S5. of Epigenetic modification with trichostatin A does not correct specific errors of somatic cell nuclear transfer at the transcriptomic level; highlighting the non-random nature of oocyte-mediated reprogramming errors

Sayyed Hosseini (3465875)
Isabelle Dufort (3465890)
Julie Nieminen (3465872)
Fariba Moulavi (2587045)
Hamid Ghanaei (3465896)
Mahdi Hajian (3465884)
Farnoosh Jafarpour (3465881)
Mohsen Forouzanfar (3465893)
Hamid Gourbai (3465869)
Abdol Shahverdi (3465887)
Mohammad Nasr-Esfahani (3465878)
Marc-André Sirard (79380)

January 2016

GO terms emerged from CTR-NT blastocyst. Gene ontology terms emerged from the differentially regulat...

Additional file 2: Table S2. of Epigenetic modification with trichostatin A does not correct specific errors of somatic cell nuclear transfer at the transcriptomic level; highlighting the non-random nature of oocyte-mediated reprogramming errors

Sayyed Hosseini (3465875)
Isabelle Dufort (3465890)
Julie Nieminen (3465872)
Fariba Moulavi (2587045)
Hamid Ghanaei (3465896)
Mahdi Hajian (3465884)
Farnoosh Jafarpour (3465881)
Mohsen Forouzanfar (3465893)
Hamid Gourbai (3465869)
Abdol Shahverdi (3465887)
Mohammad Nasr-Esfahani (3465878)
Marc-AndrĂŠ Sirard (3465899)

January 2016

CTR-NT Differentially regulated genes. Breakdown of genes differentially up and downregulated with â...

Additional file 3: Table S3. of Epigenetic modification with trichostatin A does not correct specific errors of somatic cell nuclear transfer at the transcriptomic level; highlighting the non-random nature of oocyte-mediated reprogramming errors

Sayyed Hosseini (3465875)
Isabelle Dufort (3465890)
Julie Nieminen (3465872)
Fariba Moulavi (2587045)
Hamid Ghanaei (3465896)
Mahdi Hajian (3465884)
Farnoosh Jafarpour (3465881)
Mohsen Forouzanfar (3465893)
Hamid Gourbai (3465869)
Abdol Shahverdi (3465887)
Mohammad Nasr-Esfahani (3465878)
Marc-AndrĂŠ Sirard (3465899)

January 2016

TSA-NT differentially regulated genes. Breakdown of genes differentially up and downregulated with â...

Additional file 7: Table S6. of Epigenetic modification with trichostatin A does not correct specific errors of somatic cell nuclear transfer at the transcriptomic level; highlighting the non-random nature of oocyte-mediated reprogramming errors

Sayyed Hosseini (3465875)
Isabelle Dufort (3465890)
Julie Nieminen (3465872)
Fariba Moulavi (2587045)
Hamid Ghanaei (3465896)
Mahdi Hajian (3465884)
Farnoosh Jafarpour (3465881)
Mohsen Forouzanfar (3465893)
Hamid Gourbai (3465869)
Abdol Shahverdi (3465887)
Mohammad Nasr-Esfahani (3465878)
Marc-André Sirard (79380)

January 2016

GO terms emerged from TSA-NT blastocyst. Gene ontology terms emerged from the differentially regulat...

Additional file 5: Figure S1. of Epigenetic modification with trichostatin A does not correct specific errors of somatic cell nuclear transfer at the transcriptomic level; highlighting the non-random nature of oocyte-mediated reprogramming errors

Sayyed Hosseini (3465875)
Isabelle Dufort (3465890)
Julie Nieminen (3465872)
Fariba Moulavi (2587045)
Hamid Ghanaei (3465896)
Mahdi Hajian (3465884)
Farnoosh Jafarpour (3465881)
Mohsen Forouzanfar (3465893)
Hamid Gourbai (3465869)
Abdol Shahverdi (3465887)
Mohammad Nasr-Esfahani (3465878)
Marc-André Sirard (79380)

January 2016

Nascent RNA expression in CTR-NT and TSA-NT blastocysts. A-E’) Investigation of nascent RNA expressi...

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 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. ...

Additional file 1: Table S1. of Phenotype plasticity rather than repopulation from CD90/CK14+ cancer stem cells leads to cisplatin resistance of urothelial carcinoma cell lines

Margaretha Skowron (3449309)
Günter Niegisch (3449342)
Gerhard Fritz (201905)
Tanja Arent (3449315)
Joep van Roermund (3449318)
Andrea Romano (212092)
Peter Albers (3449321)
Wolfgang Schulz (3449312)
Michèle Hoffmann (3449339)

November 2015

Primer sequences for quantitative real-time-PCR. Sequences of primers (5′-3′) used for quantitative ...

Transcriptional reprogramming of gene expression in bovine somatic cell chromatin transfer embryos

Rodriguez-Osorio, Nelida
Wang, Zhongde
Kasinathan, Poothappillai
Page, Grier P.
Robl, James M.
Memili, Erdogan

April 2009

Background: Successful reprogramming of a somatic genome to produce a healthy clone by somatic cells...

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 1: Table S1. of Gene expression analysis of pig cumulus-oocyte complexes stimulated in vitro with follicle stimulating hormone or epidermal growth factor-like peptides

Milan Blaha (3503381)
Lucie Nemcova (3503384)
Katerina Kepkova (3503375)
Petr Vodicka (3503378)
Radek Prochazka (3503387)

October 2015

List of primers used for microarray data analysis verification. List and data of primers used in qRT...

Additional file 1: of Incomplete cellular reprogramming of colorectal cancer cells elicits an epithelial/mesenchymal hybrid phenotype

Michele Hiew (5538686)
Han Cheng (475615)
Chiu-Jung Huang (3819067)
Kowit Chong (5538683)
Soon Cheong (3819064)
Kong Choo (3819061)
Tunku Kamarul (618729)

July 2018

Table S1. Primer sequences of genes and miRNAs analyzed in RT-PCR or qRT-PCR. (PDF 99 kb

Additional file 1: of The epigenetic regulation of HsMar1, a human DNA transposon

Sylvaine Renault (261575)
Murielle Genty (311750)
Alison Gabori (6339800)
Catherine Boisneau (6339803)
Charles Esnault (2386333)
Thomas DugĂŠ de Bernonville (6339806)
Corinne AugĂŠ-Gouillou (6339809)

February 2019

Data S1. Recombinant HsMar1 insertion sites in HeLa and CHO cell lines. Data S2. Inter-plasmidic act...

Additional file 3: of Transcriptional defects and reprogramming barriers in somatic cell nuclear reprogramming as revealed by single-embryo RNA sequencing

Yong Liu (6908)
Fengrui Wu (5639615)
Ling Zhang (18071)
Xiaoqing Wu (788978)
Dengkun Li (5639618)
Jing Xin (183453)
Juan Xie (461923)
Feng Kong (459884)
Wenying Wang (187565)
Qiaoqin Wu (5846117)
Di Zhang (197959)
Rong Wang (59795)
Shaorong Gao (249898)
Wenyong Li (715719)

October 2018

List of different genes between NT groups and Invivo group. Two group Ensembl gene IDs were listed. ...

Additional file 1: Table S1. of Epigenetic modification with trichostatin A does not correct specific errors of somatic cell nuclear transfer at the transcriptomic level; highlighting the non-random nature of oocyte-mediated reprogramming errors

Sayyed Hosseini (3465875)
Isabelle Dufort (3465890)
Julie Nieminen (3465872)
Fariba Moulavi (2587045)
Hamid Ghanaei (3465896)
Mahdi Hajian (3465884)
Farnoosh Jafarpour (3465881)
Mohsen Forouzanfar (3465893)
Hamid Gourbai (3465869)
Abdol Shahverdi (3465887)
Mohammad Nasr-Esfahani (3465878)
Marc-AndrĂŠ Sirard (3465899)

January 2016

Pre- and post- implantation development. Effect of TSA treatment on in vitro and in vivo development...

Additional file 6: Table S5. of Epigenetic modification with trichostatin A does not correct specific errors of somatic cell nuclear transfer at the transcriptomic level; highlighting the non-random nature of oocyte-mediated reprogramming errors

Sayyed Hosseini (3465875)
Isabelle Dufort (3465890)
Julie Nieminen (3465872)
Fariba Moulavi (2587045)
Hamid Ghanaei (3465896)
Mahdi Hajian (3465884)
Farnoosh Jafarpour (3465881)
Mohsen Forouzanfar (3465893)
Hamid Gourbai (3465869)
Abdol Shahverdi (3465887)
Mohammad Nasr-Esfahani (3465878)
Marc-André Sirard (79380)

January 2016

GO terms emerged from CTR-NT blastocyst. Gene ontology terms emerged from the differentially regulat...

Additional file 2: Table S2. of Epigenetic modification with trichostatin A does not correct specific errors of somatic cell nuclear transfer at the transcriptomic level; highlighting the non-random nature of oocyte-mediated reprogramming errors

Sayyed Hosseini (3465875)
Isabelle Dufort (3465890)
Julie Nieminen (3465872)
Fariba Moulavi (2587045)
Hamid Ghanaei (3465896)
Mahdi Hajian (3465884)
Farnoosh Jafarpour (3465881)
Mohsen Forouzanfar (3465893)
Hamid Gourbai (3465869)
Abdol Shahverdi (3465887)
Mohammad Nasr-Esfahani (3465878)
Marc-AndrĂŠ Sirard (3465899)

January 2016

CTR-NT Differentially regulated genes. Breakdown of genes differentially up and downregulated with â...

Additional file 3: Table S3. of Epigenetic modification with trichostatin A does not correct specific errors of somatic cell nuclear transfer at the transcriptomic level; highlighting the non-random nature of oocyte-mediated reprogramming errors

Sayyed Hosseini (3465875)
Isabelle Dufort (3465890)
Julie Nieminen (3465872)
Fariba Moulavi (2587045)
Hamid Ghanaei (3465896)
Mahdi Hajian (3465884)
Farnoosh Jafarpour (3465881)
Mohsen Forouzanfar (3465893)
Hamid Gourbai (3465869)
Abdol Shahverdi (3465887)
Mohammad Nasr-Esfahani (3465878)
Marc-AndrĂŠ Sirard (3465899)

January 2016

TSA-NT differentially regulated genes. Breakdown of genes differentially up and downregulated with â...

Additional file 7: Table S6. of Epigenetic modification with trichostatin A does not correct specific errors of somatic cell nuclear transfer at the transcriptomic level; highlighting the non-random nature of oocyte-mediated reprogramming errors

Sayyed Hosseini (3465875)
Isabelle Dufort (3465890)
Julie Nieminen (3465872)
Fariba Moulavi (2587045)
Hamid Ghanaei (3465896)
Mahdi Hajian (3465884)
Farnoosh Jafarpour (3465881)
Mohsen Forouzanfar (3465893)
Hamid Gourbai (3465869)
Abdol Shahverdi (3465887)
Mohammad Nasr-Esfahani (3465878)
Marc-André Sirard (79380)

January 2016

GO terms emerged from TSA-NT blastocyst. Gene ontology terms emerged from the differentially regulat...

Additional file 5: Figure S1. of Epigenetic modification with trichostatin A does not correct specific errors of somatic cell nuclear transfer at the transcriptomic level; highlighting the non-random nature of oocyte-mediated reprogramming errors

Sayyed Hosseini (3465875)
Isabelle Dufort (3465890)
Julie Nieminen (3465872)
Fariba Moulavi (2587045)
Hamid Ghanaei (3465896)
Mahdi Hajian (3465884)
Farnoosh Jafarpour (3465881)
Mohsen Forouzanfar (3465893)
Hamid Gourbai (3465869)
Abdol Shahverdi (3465887)
Mohammad Nasr-Esfahani (3465878)
Marc-André Sirard (79380)

January 2016

Nascent RNA expression in CTR-NT and TSA-NT blastocysts. A-E’) Investigation of nascent RNA expressi...

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 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. ...

Additional file 1: Table S1. of Phenotype plasticity rather than repopulation from CD90/CK14+ cancer stem cells leads to cisplatin resistance of urothelial carcinoma cell lines

Margaretha Skowron (3449309)
Günter Niegisch (3449342)
Gerhard Fritz (201905)
Tanja Arent (3449315)
Joep van Roermund (3449318)
Andrea Romano (212092)
Peter Albers (3449321)
Wolfgang Schulz (3449312)
Michèle Hoffmann (3449339)

November 2015

Primer sequences for quantitative real-time-PCR. Sequences of primers (5′-3′) used for quantitative ...

Transcriptional reprogramming of gene expression in bovine somatic cell chromatin transfer embryos

Rodriguez-Osorio, Nelida
Wang, Zhongde
Kasinathan, Poothappillai
Page, Grier P.
Robl, James M.
Memili, Erdogan

April 2009

Background: Successful reprogramming of a somatic genome to produce a healthy clone by somatic cells...

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 1: Table S1. of Gene expression analysis of pig cumulus-oocyte complexes stimulated in vitro with follicle stimulating hormone or epidermal growth factor-like peptides

Milan Blaha (3503381)
Lucie Nemcova (3503384)
Katerina Kepkova (3503375)
Petr Vodicka (3503378)
Radek Prochazka (3503387)

October 2015

List of primers used for microarray data analysis verification. List and data of primers used in qRT...

Additional file 1: of Incomplete cellular reprogramming of colorectal cancer cells elicits an epithelial/mesenchymal hybrid phenotype

Michele Hiew (5538686)
Han Cheng (475615)
Chiu-Jung Huang (3819067)
Kowit Chong (5538683)
Soon Cheong (3819064)
Kong Choo (3819061)
Tunku Kamarul (618729)

July 2018

Table S1. Primer sequences of genes and miRNAs analyzed in RT-PCR or qRT-PCR. (PDF 99 kb

Additional file 1: of The epigenetic regulation of HsMar1, a human DNA transposon

Sylvaine Renault (261575)
Murielle Genty (311750)
Alison Gabori (6339800)
Catherine Boisneau (6339803)
Charles Esnault (2386333)
Thomas DugĂŠ de Bernonville (6339806)
Corinne AugĂŠ-Gouillou (6339809)

February 2019

Data S1. Recombinant HsMar1 insertion sites in HeLa and CHO cell lines. Data S2. Inter-plasmidic act...

Additional file 3: of Transcriptional defects and reprogramming barriers in somatic cell nuclear reprogramming as revealed by single-embryo RNA sequencing

Yong Liu (6908)
Fengrui Wu (5639615)
Ling Zhang (18071)
Xiaoqing Wu (788978)
Dengkun Li (5639618)
Jing Xin (183453)
Juan Xie (461923)
Feng Kong (459884)
Wenying Wang (187565)
Qiaoqin Wu (5846117)
Di Zhang (197959)
Rong Wang (59795)
Shaorong Gao (249898)
Wenyong Li (715719)

October 2018

List of different genes between NT groups and Invivo group. Two group Ensembl gene IDs were listed. ...

Additional file 9: Table S8. of Epigenetic modification with trichostatin A does not correct specific errors of somatic cell nuclear transfer at the transcriptomic level; highlighting the non-random nature of oocyte-mediated reprogramming errors

Abstract

Extracted data

Additional file 9: Table S8. of Epigenetic modification with trichostatin A does not correct specific errors of somatic cell nuclear transfer at the transcriptomic level; highlighting the non-random nature of oocyte-mediated reprogramming errors

Abstract

Extracted data

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