Additional file 3: of Disrupted circadian clocks and altered tissue mechanics in primary human breast tumours

Additional file 3: Figure S3. of Inhibition of basal-like breast cancer growth by FTY720 in combination with epidermal growth factor receptor kinase blockade

Janet Martin (3022770)
Sohel Julovi (4333738)
Mike Lin (4333741)
Hasanthi de Silva (4333744)
Frances Boyle (505085)
Robert Baxter (102239)

August 2017

CD3 levels in 4T1 tumors grown in wild-type BALB/c mice. Samples were from the experiment shown in F...

Additional file 1: of Gene expression modules in primary breast cancers as risk factors for organotropic patterns of first metastatic spread: a case control study

Katherine Lawler (4513297)
Efterpi Papouli (553691)
Cristina Naceur-Lombardelli (4513306)
Anca Mera (4513309)
Kayleigh Ougham (4513300)
Andrew Tutt (245167)
Siker Kimbung (630325)
Ingrid Hedenfalk (75489)
Jun Zhan (296663)
Hongquan Zhang (61781)
Richard Buus (373008)
Mitch Dowsett (645)
Tony Ng (172369)
Sarah Pinder (553692)
Peter Parker (668602)
Lars Holmberg (73013)
Cheryl Gillett (553699)
Anita Grigoriadis (41195)
Arnie Purushotham (4513303)

October 2017

Supplementary methods. Detailed description of tissue preparation including microtomy, de-waxing and...

Additional file 2: of Functional genomics identifies specific vulnerabilities in PTEN-deficient breast cancer

Yew Tang (4996598)
Szu-Chi Ho (4996595)
Elisabeth Tan (4996589)
Alvin Ng (270121)
John McPherson (545720)
Germaine Goh (798727)
Bin Teh (3548891)
Frederic Bard (798730)
Steven Rozen (4996592)

March 2018

Figure S1. PTEN protein abundance of breast cancer cell lines. (A) Western blots showing PTEN and ac...

Additional file 1: of Disrupted circadian clocks and altered tissue mechanics in primary human breast tumours

Eleanor Broadberry (5881016)
James McConnell (3487649)
Jack Williams (52430)
Nan Yang (305078)
Egor Zindy (2656738)
Angela Leek (3487679)
Rachel Waddington (5881019)
Leena Joseph (180330)
Miles Howe (3487661)
Qing-Jun Meng (179045)
Charles Streuli (3487652)

October 2018

Figure S1. Breast tissues used in this study. Mammograms of patients examined in this study. The reg...

Additional file 6: of Disrupted circadian clocks and altered tissue mechanics in primary human breast tumours

Eleanor Broadberry (5881016)
James McConnell (3487649)
Jack Williams (52430)
Nan Yang (305078)
Egor Zindy (2656738)
Angela Leek (3487679)
Rachel Waddington (5881019)
Leena Joseph (180330)
Miles Howe (3487661)
Qing-Jun Meng (179045)
Charles Streuli (3487652)

October 2018

Figure S6. Stromal regions analysed by AFM. H&E staining of the normal and tumour regions of breasts...

Additional file 4: of Disrupted circadian clocks and altered tissue mechanics in primary human breast tumours

Eleanor Broadberry (5881016)
James McConnell (3487649)
Jack Williams (52430)
Nan Yang (305078)
Egor Zindy (2656738)
Angela Leek (3487679)
Rachel Waddington (5881019)
Leena Joseph (180330)
Miles Howe (3487661)
Qing-Jun Meng (179045)
Charles Streuli (3487652)

October 2018

Figure S4. Circadian clocks in breast tissue. Left - representative Per2::Luc traces from cultures o...

Additional file 5: of Disrupted circadian clocks and altered tissue mechanics in primary human breast tumours

Eleanor Broadberry (5881016)
James McConnell (3487649)
Jack Williams (52430)
Nan Yang (305078)
Egor Zindy (2656738)
Angela Leek (3487679)
Rachel Waddington (5881019)
Leena Joseph (180330)
Miles Howe (3487661)
Qing-Jun Meng (179045)
Charles Streuli (3487652)

October 2018

Figure S5. Collagen organisation in normal and tumour stroma. Picrosirius-Red-stained paraffin secti...

Additional file 1: of Circadian oscillations of cytosine modification in humans contribute to epigenetic variability, aging, and complex disease

Gabriel Oh (3448379)
Karolis Koncevičius (6173486)
Sasha Ebrahimi (3448385)
Matthew Carlucci (6173489)
Daniel Groot (6173492)
Akhil Nair (6173495)
Aiping Zhang (448556)
Algimantas Kriščiūnas (6173498)
Edward Oh (6173501)
Viviane Labrie (6173504)
Albert Wong (365470)
Juozas Gordevičius (6173507)
Peixin Jia (6173510)
Miki Susic (6173513)
Art Petronis (3448373)

January 2019

Oscillation parameters of white blood cell fractions. Counts, fractions, and oscillation p values of...

Additional file 3: of Circadian oscillations of cytosine modification in humans contribute to epigenetic variability, aging, and complex disease

Gabriel Oh (3448379)
Karolis Koncevičius (6173486)
Sasha Ebrahimi (3448385)
Matthew Carlucci (6173489)
Daniel Groot (6173492)
Akhil Nair (6173495)
Aiping Zhang (448556)
Algimantas Kriščiūnas (6173498)
Edward Oh (6173501)
Viviane Labrie (6173504)
Albert Wong (365470)
Juozas Gordevičius (6173507)
Peixin Jia (6173510)
Miki Susic (6173513)
Art Petronis (3448373)

January 2019

Proportion of variance explained by oscillations at various EVCs thresholds. Number of total EVCs, p...

Additional file 3: of Evaluation of α-tubulin, detyrosinated α-tubulin, and vimentin in CTCs: identification of the interaction between CTCs and blood cells through cytoskeletal elements

G. Kallergi (5486657)
D. Aggouraki (5486654)
N. Zacharopoulou (5486651)
C. Stournaras (5486645)
V. Georgoulias (5486648)
S. Martin (1435966)

July 2018

Single CTC distribution regarding CK/TUB, CK/VIM, and CK/GLU ratios. CK/TUB ratio in CTCs obtained f...

Additional file 2: of Circadian oscillations of cytosine modification in humans contribute to epigenetic variability, aging, and complex disease

Gabriel Oh (3448379)
Karolis Koncevičius (6173486)
Sasha Ebrahimi (3448385)
Matthew Carlucci (6173489)
Daniel Groot (6173492)
Akhil Nair (6173495)
Aiping Zhang (448556)
Algimantas Kriščiūnas (6173498)
Edward Oh (6173501)
Viviane Labrie (6173504)
Albert Wong (365470)
Juozas Gordevičius (6173507)
Peixin Jia (6173510)
Miki Susic (6173513)
Art Petronis (3448373)

January 2019

Oscillation parameters for all interrogated CpG positions. EVC p value, cosinor p value, mesor, acro...

Additional file 3: Table S3. of Circadian pathway genetic variation and cancer risk: evidence from genome-wide association studies

Simone Mocellin (362633)
Saveria Tropea (4862188)
Clara Benna (464728)
Carlo Rossi (222320)

February 2018

Adaptive rank truncated product (ARTP)-based analysis of single circadian genes: subgroup analysis (...

Additional file 7: of Circadian oscillations of cytosine modification in humans contribute to epigenetic variability, aging, and complex disease

Gabriel Oh (3448379)
Karolis Koncevičius (6173486)
Sasha Ebrahimi (3448385)
Matthew Carlucci (6173489)
Daniel Groot (6173492)
Akhil Nair (6173495)
Aiping Zhang (448556)
Algimantas Kriščiūnas (6173498)
Edward Oh (6173501)
Viviane Labrie (6173504)
Albert Wong (365470)
Juozas Gordevičius (6173507)
Peixin Jia (6173510)
Miki Susic (6173513)
Art Petronis (3448373)

January 2019

TOMTOM output for hyper-variable cytosines from populational neutrophil data. Motifs detected from s...

Additional file 10: of GSK3β regulates epithelial-mesenchymal transition and cancer stem cell properties in triple-negative breast cancer

Geraldine Vijay (6437930)
Na Zhao (112953)
Petra Hollander (6437933)
Mike Toneff (6437936)
Robiya Joseph (6437939)
Mika Pietila (6437942)
Joseph Taube (4458358)
Tapasree Sarkar (6437945)
Esmeralda Ramirez-Pena (6437948)
Steven Werden (6437951)
Maryam Shariati (4043501)
Ruli Gao (6437954)
Mary Sobieski (5690516)
Clifford Stephan (6437957)
Nathalie Sphyris (6437960)
Noayuki Miura (6437963)
Peter Davies (95719)
Jeffrey Chang (3945326)
Rama Soundararajan (6437966)
Jeffrey Rosen (3172593)
Sendurai Mani (4043519)

March 2019

Figure S8. Claudin-low T11 cells were grown in ultra-low attachment plates in mammosphere media for ...

Comparison of circadian gene expression in the breast cancer tissue samples and the tumor-adjacent normal tissue samples.

Monika Lesicka (5470358)
Ewa Jabłońska (2496328)
Edyta Wieczorek (3432455)
Barbara Seroczyńska (548473)
Anna Siekierzycka (5470355)
Jarosław Skokowski (443461)
Leszek Kalinowski (4568038)
Wojciech Wąsowicz (3533090)
Edyta Reszka (3432440)

June 2018

<p>Comparison of circadian gene expression in the breast cancer tissue samples and the tumor-adjacen...

Additional file 3: Figure S3. of Inhibition of basal-like breast cancer growth by FTY720 in combination with epidermal growth factor receptor kinase blockade

Janet Martin (3022770)
Sohel Julovi (4333738)
Mike Lin (4333741)
Hasanthi de Silva (4333744)
Frances Boyle (505085)
Robert Baxter (102239)

August 2017

CD3 levels in 4T1 tumors grown in wild-type BALB/c mice. Samples were from the experiment shown in F...

Additional file 1: of Gene expression modules in primary breast cancers as risk factors for organotropic patterns of first metastatic spread: a case control study

Katherine Lawler (4513297)
Efterpi Papouli (553691)
Cristina Naceur-Lombardelli (4513306)
Anca Mera (4513309)
Kayleigh Ougham (4513300)
Andrew Tutt (245167)
Siker Kimbung (630325)
Ingrid Hedenfalk (75489)
Jun Zhan (296663)
Hongquan Zhang (61781)
Richard Buus (373008)
Mitch Dowsett (645)
Tony Ng (172369)
Sarah Pinder (553692)
Peter Parker (668602)
Lars Holmberg (73013)
Cheryl Gillett (553699)
Anita Grigoriadis (41195)
Arnie Purushotham (4513303)

October 2017

Supplementary methods. Detailed description of tissue preparation including microtomy, de-waxing and...

Additional file 2: of Functional genomics identifies specific vulnerabilities in PTEN-deficient breast cancer

Yew Tang (4996598)
Szu-Chi Ho (4996595)
Elisabeth Tan (4996589)
Alvin Ng (270121)
John McPherson (545720)
Germaine Goh (798727)
Bin Teh (3548891)
Frederic Bard (798730)
Steven Rozen (4996592)

March 2018

Figure S1. PTEN protein abundance of breast cancer cell lines. (A) Western blots showing PTEN and ac...

Additional file 1: of Disrupted circadian clocks and altered tissue mechanics in primary human breast tumours

Eleanor Broadberry (5881016)
James McConnell (3487649)
Jack Williams (52430)
Nan Yang (305078)
Egor Zindy (2656738)
Angela Leek (3487679)
Rachel Waddington (5881019)
Leena Joseph (180330)
Miles Howe (3487661)
Qing-Jun Meng (179045)
Charles Streuli (3487652)

October 2018

Figure S1. Breast tissues used in this study. Mammograms of patients examined in this study. The reg...

Additional file 6: of Disrupted circadian clocks and altered tissue mechanics in primary human breast tumours

Eleanor Broadberry (5881016)
James McConnell (3487649)
Jack Williams (52430)
Nan Yang (305078)
Egor Zindy (2656738)
Angela Leek (3487679)
Rachel Waddington (5881019)
Leena Joseph (180330)
Miles Howe (3487661)
Qing-Jun Meng (179045)
Charles Streuli (3487652)

October 2018

Figure S6. Stromal regions analysed by AFM. H&E staining of the normal and tumour regions of breasts...

Additional file 4: of Disrupted circadian clocks and altered tissue mechanics in primary human breast tumours

Eleanor Broadberry (5881016)
James McConnell (3487649)
Jack Williams (52430)
Nan Yang (305078)
Egor Zindy (2656738)
Angela Leek (3487679)
Rachel Waddington (5881019)
Leena Joseph (180330)
Miles Howe (3487661)
Qing-Jun Meng (179045)
Charles Streuli (3487652)

October 2018

Figure S4. Circadian clocks in breast tissue. Left - representative Per2::Luc traces from cultures o...

Additional file 5: of Disrupted circadian clocks and altered tissue mechanics in primary human breast tumours

Eleanor Broadberry (5881016)
James McConnell (3487649)
Jack Williams (52430)
Nan Yang (305078)
Egor Zindy (2656738)
Angela Leek (3487679)
Rachel Waddington (5881019)
Leena Joseph (180330)
Miles Howe (3487661)
Qing-Jun Meng (179045)
Charles Streuli (3487652)

October 2018

Figure S5. Collagen organisation in normal and tumour stroma. Picrosirius-Red-stained paraffin secti...

Additional file 1: of Circadian oscillations of cytosine modification in humans contribute to epigenetic variability, aging, and complex disease

Gabriel Oh (3448379)
Karolis Koncevičius (6173486)
Sasha Ebrahimi (3448385)
Matthew Carlucci (6173489)
Daniel Groot (6173492)
Akhil Nair (6173495)
Aiping Zhang (448556)
Algimantas Kriščiūnas (6173498)
Edward Oh (6173501)
Viviane Labrie (6173504)
Albert Wong (365470)
Juozas Gordevičius (6173507)
Peixin Jia (6173510)
Miki Susic (6173513)
Art Petronis (3448373)

January 2019

Oscillation parameters of white blood cell fractions. Counts, fractions, and oscillation p values of...

Additional file 3: of Circadian oscillations of cytosine modification in humans contribute to epigenetic variability, aging, and complex disease

Gabriel Oh (3448379)
Karolis Koncevičius (6173486)
Sasha Ebrahimi (3448385)
Matthew Carlucci (6173489)
Daniel Groot (6173492)
Akhil Nair (6173495)
Aiping Zhang (448556)
Algimantas Kriščiūnas (6173498)
Edward Oh (6173501)
Viviane Labrie (6173504)
Albert Wong (365470)
Juozas Gordevičius (6173507)
Peixin Jia (6173510)
Miki Susic (6173513)
Art Petronis (3448373)

January 2019

Proportion of variance explained by oscillations at various EVCs thresholds. Number of total EVCs, p...

Additional file 3: of Evaluation of α-tubulin, detyrosinated α-tubulin, and vimentin in CTCs: identification of the interaction between CTCs and blood cells through cytoskeletal elements

G. Kallergi (5486657)
D. Aggouraki (5486654)
N. Zacharopoulou (5486651)
C. Stournaras (5486645)
V. Georgoulias (5486648)
S. Martin (1435966)

July 2018

Single CTC distribution regarding CK/TUB, CK/VIM, and CK/GLU ratios. CK/TUB ratio in CTCs obtained f...

Additional file 2: of Circadian oscillations of cytosine modification in humans contribute to epigenetic variability, aging, and complex disease

Gabriel Oh (3448379)
Karolis Koncevičius (6173486)
Sasha Ebrahimi (3448385)
Matthew Carlucci (6173489)
Daniel Groot (6173492)
Akhil Nair (6173495)
Aiping Zhang (448556)
Algimantas Kriščiūnas (6173498)
Edward Oh (6173501)
Viviane Labrie (6173504)
Albert Wong (365470)
Juozas Gordevičius (6173507)
Peixin Jia (6173510)
Miki Susic (6173513)
Art Petronis (3448373)

January 2019

Oscillation parameters for all interrogated CpG positions. EVC p value, cosinor p value, mesor, acro...

Additional file 3: Table S3. of Circadian pathway genetic variation and cancer risk: evidence from genome-wide association studies

Simone Mocellin (362633)
Saveria Tropea (4862188)
Clara Benna (464728)
Carlo Rossi (222320)

February 2018

Adaptive rank truncated product (ARTP)-based analysis of single circadian genes: subgroup analysis (...

Additional file 7: of Circadian oscillations of cytosine modification in humans contribute to epigenetic variability, aging, and complex disease

Gabriel Oh (3448379)
Karolis Koncevičius (6173486)
Sasha Ebrahimi (3448385)
Matthew Carlucci (6173489)
Daniel Groot (6173492)
Akhil Nair (6173495)
Aiping Zhang (448556)
Algimantas Kriščiūnas (6173498)
Edward Oh (6173501)
Viviane Labrie (6173504)
Albert Wong (365470)
Juozas Gordevičius (6173507)
Peixin Jia (6173510)
Miki Susic (6173513)
Art Petronis (3448373)

January 2019

TOMTOM output for hyper-variable cytosines from populational neutrophil data. Motifs detected from s...

Additional file 10: of GSK3β regulates epithelial-mesenchymal transition and cancer stem cell properties in triple-negative breast cancer

Geraldine Vijay (6437930)
Na Zhao (112953)
Petra Hollander (6437933)
Mike Toneff (6437936)
Robiya Joseph (6437939)
Mika Pietila (6437942)
Joseph Taube (4458358)
Tapasree Sarkar (6437945)
Esmeralda Ramirez-Pena (6437948)
Steven Werden (6437951)
Maryam Shariati (4043501)
Ruli Gao (6437954)
Mary Sobieski (5690516)
Clifford Stephan (6437957)
Nathalie Sphyris (6437960)
Noayuki Miura (6437963)
Peter Davies (95719)
Jeffrey Chang (3945326)
Rama Soundararajan (6437966)
Jeffrey Rosen (3172593)
Sendurai Mani (4043519)

March 2019

Figure S8. Claudin-low T11 cells were grown in ultra-low attachment plates in mammosphere media for ...

Comparison of circadian gene expression in the breast cancer tissue samples and the tumor-adjacent normal tissue samples.

Monika Lesicka (5470358)
Ewa Jabłońska (2496328)
Edyta Wieczorek (3432455)
Barbara Seroczyńska (548473)
Anna Siekierzycka (5470355)
Jarosław Skokowski (443461)
Leszek Kalinowski (4568038)
Wojciech Wąsowicz (3533090)
Edyta Reszka (3432440)

June 2018

<p>Comparison of circadian gene expression in the breast cancer tissue samples and the tumor-adjacen...

Additional file 3: Figure S3. of Inhibition of basal-like breast cancer growth by FTY720 in combination with epidermal growth factor receptor kinase blockade

Janet Martin (3022770)
Sohel Julovi (4333738)
Mike Lin (4333741)
Hasanthi de Silva (4333744)
Frances Boyle (505085)
Robert Baxter (102239)

August 2017

CD3 levels in 4T1 tumors grown in wild-type BALB/c mice. Samples were from the experiment shown in F...

Additional file 1: of Gene expression modules in primary breast cancers as risk factors for organotropic patterns of first metastatic spread: a case control study

Katherine Lawler (4513297)
Efterpi Papouli (553691)
Cristina Naceur-Lombardelli (4513306)
Anca Mera (4513309)
Kayleigh Ougham (4513300)
Andrew Tutt (245167)
Siker Kimbung (630325)
Ingrid Hedenfalk (75489)
Jun Zhan (296663)
Hongquan Zhang (61781)
Richard Buus (373008)
Mitch Dowsett (645)
Tony Ng (172369)
Sarah Pinder (553692)
Peter Parker (668602)
Lars Holmberg (73013)
Cheryl Gillett (553699)
Anita Grigoriadis (41195)
Arnie Purushotham (4513303)

October 2017

Supplementary methods. Detailed description of tissue preparation including microtomy, de-waxing and...

Additional file 2: of Functional genomics identifies specific vulnerabilities in PTEN-deficient breast cancer

Yew Tang (4996598)
Szu-Chi Ho (4996595)
Elisabeth Tan (4996589)
Alvin Ng (270121)
John McPherson (545720)
Germaine Goh (798727)
Bin Teh (3548891)
Frederic Bard (798730)
Steven Rozen (4996592)

March 2018

Figure S1. PTEN protein abundance of breast cancer cell lines. (A) Western blots showing PTEN and ac...

Additional file 3: of Disrupted circadian clocks and altered tissue mechanics in primary human breast tumours

Abstract

Extracted data

Additional file 3: of Disrupted circadian clocks and altered tissue mechanics in primary human breast tumours

Abstract

Extracted data

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