Additional file 7: of Comparison of triple-negative breast cancer molecular subtyping using RNA from matched fresh-frozen versus formalin-fixed paraffin-embedded tissue

Additional file 1: of RNA-sequencing in non-small cell lung cancer shows gene downregulation of therapeutic targets in tumor tissue compared to non-malignant lung tissue

Kobe Reynders (5526461)
Els Wauters (101718)
Matthieu Moisse (659185)
Herbert DecaluwĂŠ (5526488)
Paul De Leyn (5526455)
StĂŠphanie Peeters (5526485)
Maarten Lambrecht (5526458)
Kristiaan Nackaerts (3210705)
Christophe Dooms (2938749)
Wim Janssens (101722)
Johan Vansteenkiste (5526467)
Diether Lambrechts (101772)
Dirk De Ruysscher (810406)

July 2018

Table S1. RNA-sequencing results for tumor tissue (a) or non-malignant lung tissue (b). Differential...

Additional file 7: of Separation of breast cancer and organ microenvironment transcriptomes in metastases

Mohammad Alzubi (6431630)
Tia Turner (6431633)
Amy Olex (6431636)
Sahib Sohal (6431639)
Nicholas Tobin (4848271)
Susana Recio (6431642)
Jonas Bergh (23551)
Thomas Hatschek (22685)
Joel Parker (17174)
Carol Sartorius (6431645)
Charles Perou (3530138)
Mikhail Dozmorov (4630)
J. Harrell (6413768)

March 2019

Genes upregulated during liver metastasis; cancer and organ-specific changes. DESeq2 was used to ide...

Additional file 7: of Identification of three subtypes of triple-negative breast cancer with potential therapeutic implications

Pascal Jézéquel (217021)
Olivier Kerdraon (6711944)
Hubert Hondermarck (3624869)
Catherine Guérin-Charbonnel (3399809)
Hamza Lasla (3399812)
Wilfried Gouraud (3399800)
Jean-Luc Canon (2587597)
Andrea Gombos (3147276)
Florence Dalenc (15454)
Suzette Delaloge (805610)
Jérôme Lemonnier (5845856)
Delphine Loussouarn (128055)
Véronique Verrièle (6711947)
Mario Campone (217018)

May 2019

Projection of internal TNBC cohort in the first PCA plane. (C1, n = 55 [blue]; C2, n = 98 [red]; C3,...

Additional file 3: of Comparison of triple-negative breast cancer molecular subtyping using RNA from matched fresh-frozen versus formalin-fixed paraffin-embedded tissue

Bojana JovanoviÄ (3904495)
Quanhu Sheng (448059)
Robert Seitz (3904483)
Kasey Lawrence (3904489)
Stephan Morris (3904477)
Lance Thomas (3904480)
David Hout (3904474)
Brock Schweitzer (3904471)
Yan Guo (83742)
Jennifer Pietenpol (3904486)
Brian Lehmann (3904492)

April 2017

Table S2. Samples sequenced. Sample type, processing and sequencing. (XLSX 51Â kb

Additional file 4: of Comparison of triple-negative breast cancer molecular subtyping using RNA from matched fresh-frozen versus formalin-fixed paraffin-embedded tissue

Bojana JovanoviÄ (3904495)
Quanhu Sheng (448059)
Robert Seitz (3904483)
Kasey Lawrence (3904489)
Stephan Morris (3904477)
Lance Thomas (3904480)
David Hout (3904474)
Brock Schweitzer (3904471)
Yan Guo (83742)
Jennifer Pietenpol (3904486)
Brian Lehmann (3904492)

April 2017

Figure S2. Comparison of read alignment for FF- and FFPE-derived RNA samples sequenced on MiSeq and ...

Additional file 5: of Comparison of triple-negative breast cancer molecular subtyping using RNA from matched fresh-frozen versus formalin-fixed paraffin-embedded tissue

Bojana JovanoviÄ (3904495)
Quanhu Sheng (448059)
Robert Seitz (3904483)
Kasey Lawrence (3904489)
Stephan Morris (3904477)
Lance Thomas (3904480)
David Hout (3904474)
Brock Schweitzer (3904471)
Yan Guo (83742)
Jennifer Pietenpol (3904486)
Brian Lehmann (3904492)

April 2017

Figure S3. Specimen age correlation. Tumor specimen age decreases transcript correlation of sequence...

Additional file 3: of Progression-specific genes identified in microdissected formalin-fixed and paraffin-embedded tissue containing matched ductal carcinoma in situ and invasive ductal breast cancers

Silke Schultz (5776364)
Harald Bartsch (5776367)
Karl Sotlar (23621)
Karina Petat-Dutter (5776376)
Michael Bonin (161261)
Steffen Kahlert (2721343)
Nadia Harbeck (5106476)
Ulrich Vogel (37785)
Harald Seeger (72128)
Tanja Fehm (23618)
Hans Neubauer (23624)

September 2018

Validation 5 FFPE samples analogue to FF samples, Description: A) Analogue samples FFPE-Cryo: The se...

Additional file 3: of Assessing breast cancer cell lines as tumour models by comparison of mRNA expression profiles

Krista Vincent (3576728)
Scott Findlay (3576725)
Lynne Postovit (3576731)

August 2015

Top 1 % of differentially expressed genes between tumours and cell lines after filtering out genes c...

Additional file 7: of Integrated proteotranscriptomics of breast cancer reveals globally increased protein-mRNA concordance associated with subtypes and survival

Wei Tang (53470)
Ming Zhou (73279)
Tiffany Dorsey (6036011)
DaRue Prieto (6036014)
Xin Wang (91924)
Eytan Ruppin (23002)
Timothy Veenstra (113151)
Stefan Ambs (37080)

December 2018

Tables S5. Significantly differentially expressed proteins between breast tumors and adjacent non-ca...

Additional file 3: of Classification of triple-negative breast cancers based on Immunogenomic profiling

Yin He (120155)
Zehang Jiang (6164414)
Cai Chen (181184)
Xiaosheng Wang (553236)

December 2018

Figure S2. Comparisons of the expression levels of immune-related genes between TNBC subtypes. A. Co...

Additional file 4: of Assessing breast cancer cell lines as tumour models by comparison of mRNA expression profiles

Krista Vincent (3576728)
Scott Findlay (3576725)
Lynne Postovit (3576731)

August 2015

Comparison of the frequency of select mutational events in breast cancer tumours versus cell lines. ...

Additional file 2: of Assessing breast cancer cell lines as tumour models by comparison of mRNA expression profiles

Krista Vincent (3576728)
Scott Findlay (3576725)
Lynne Postovit (3576731)

August 2015

Top 1 % of differentially expressed genes between tumours and cell lines (with adjusted p values by ...

Additional file 2: of Classification of triple-negative breast cancers based on Immunogenomic profiling

Yin He (120155)
Zehang Jiang (6164414)
Cai Chen (181184)
Xiaosheng Wang (553236)

December 2018

Figure S1. Comparisons of the stromal content and tumor purity between TNBC subtypes (MannâWhitney...

Additional file 3: of Molecular biomarkers screened by next-generation RNA sequencing for non-sentinel lymph node status prediction in breast cancer patients with metastatic sentinel lymph nodes

Feng Liang (447805)
Hongzhu Qu (36515)
Qiang Lin (208776)
Yadong Yang (396824)
Xiuyan Ruan (3450233)
Bo Zhang (6559)
Yi Liu (36759)
Chengze Yu (3450230)
Hongyan Zhang (618068)
Xiangdong Fang (180671)
Xiaopeng Hao (1644652)

August 2015

Scatter plots of gene expression values between samples. A figure illustrating how similar of genes ...

Additional file 3: of The association of genomic lesions and PD-1/PD-L1 expression in resected triple-negative breast cancers

Michael Barrett (128123)
Elizabeth Lenkiewicz (117033)
Smriti Malasi (5505893)
Anamika Basu (334844)
Jennifer Yearley (5505899)
Lakshmanan Annamalai (358396)
Ann McCullough (5505890)
Heidi Kosiorek (5505896)
Pooja Narang (298385)
Melissa Wilson Sayres (5505905)
Meixuan Chen (5505902)
Karen Anderson (217635)
Barbara Pockaj (117056)

July 2018

Figure S3. Flow-sorting fresh frozen (FF) TNBC tissue samples. DNA content analysis of diploid and a...

Additional file 1: of RNA-sequencing in non-small cell lung cancer shows gene downregulation of therapeutic targets in tumor tissue compared to non-malignant lung tissue

Kobe Reynders (5526461)
Els Wauters (101718)
Matthieu Moisse (659185)
Herbert DecaluwĂŠ (5526488)
Paul De Leyn (5526455)
StĂŠphanie Peeters (5526485)
Maarten Lambrecht (5526458)
Kristiaan Nackaerts (3210705)
Christophe Dooms (2938749)
Wim Janssens (101722)
Johan Vansteenkiste (5526467)
Diether Lambrechts (101772)
Dirk De Ruysscher (810406)

July 2018

Table S1. RNA-sequencing results for tumor tissue (a) or non-malignant lung tissue (b). Differential...

Additional file 7: of Separation of breast cancer and organ microenvironment transcriptomes in metastases

Mohammad Alzubi (6431630)
Tia Turner (6431633)
Amy Olex (6431636)
Sahib Sohal (6431639)
Nicholas Tobin (4848271)
Susana Recio (6431642)
Jonas Bergh (23551)
Thomas Hatschek (22685)
Joel Parker (17174)
Carol Sartorius (6431645)
Charles Perou (3530138)
Mikhail Dozmorov (4630)
J. Harrell (6413768)

March 2019

Genes upregulated during liver metastasis; cancer and organ-specific changes. DESeq2 was used to ide...

Additional file 7: of Identification of three subtypes of triple-negative breast cancer with potential therapeutic implications

Pascal Jézéquel (217021)
Olivier Kerdraon (6711944)
Hubert Hondermarck (3624869)
Catherine Guérin-Charbonnel (3399809)
Hamza Lasla (3399812)
Wilfried Gouraud (3399800)
Jean-Luc Canon (2587597)
Andrea Gombos (3147276)
Florence Dalenc (15454)
Suzette Delaloge (805610)
Jérôme Lemonnier (5845856)
Delphine Loussouarn (128055)
Véronique Verrièle (6711947)
Mario Campone (217018)

May 2019

Projection of internal TNBC cohort in the first PCA plane. (C1, n = 55 [blue]; C2, n = 98 [red]; C3,...

Additional file 3: of Comparison of triple-negative breast cancer molecular subtyping using RNA from matched fresh-frozen versus formalin-fixed paraffin-embedded tissue

Bojana JovanoviÄ (3904495)
Quanhu Sheng (448059)
Robert Seitz (3904483)
Kasey Lawrence (3904489)
Stephan Morris (3904477)
Lance Thomas (3904480)
David Hout (3904474)
Brock Schweitzer (3904471)
Yan Guo (83742)
Jennifer Pietenpol (3904486)
Brian Lehmann (3904492)

April 2017

Table S2. Samples sequenced. Sample type, processing and sequencing. (XLSX 51Â kb

Additional file 4: of Comparison of triple-negative breast cancer molecular subtyping using RNA from matched fresh-frozen versus formalin-fixed paraffin-embedded tissue

Bojana JovanoviÄ (3904495)
Quanhu Sheng (448059)
Robert Seitz (3904483)
Kasey Lawrence (3904489)
Stephan Morris (3904477)
Lance Thomas (3904480)
David Hout (3904474)
Brock Schweitzer (3904471)
Yan Guo (83742)
Jennifer Pietenpol (3904486)
Brian Lehmann (3904492)

April 2017

Figure S2. Comparison of read alignment for FF- and FFPE-derived RNA samples sequenced on MiSeq and ...

Additional file 5: of Comparison of triple-negative breast cancer molecular subtyping using RNA from matched fresh-frozen versus formalin-fixed paraffin-embedded tissue

Bojana JovanoviÄ (3904495)
Quanhu Sheng (448059)
Robert Seitz (3904483)
Kasey Lawrence (3904489)
Stephan Morris (3904477)
Lance Thomas (3904480)
David Hout (3904474)
Brock Schweitzer (3904471)
Yan Guo (83742)
Jennifer Pietenpol (3904486)
Brian Lehmann (3904492)

April 2017

Figure S3. Specimen age correlation. Tumor specimen age decreases transcript correlation of sequence...

Additional file 3: of Progression-specific genes identified in microdissected formalin-fixed and paraffin-embedded tissue containing matched ductal carcinoma in situ and invasive ductal breast cancers

Silke Schultz (5776364)
Harald Bartsch (5776367)
Karl Sotlar (23621)
Karina Petat-Dutter (5776376)
Michael Bonin (161261)
Steffen Kahlert (2721343)
Nadia Harbeck (5106476)
Ulrich Vogel (37785)
Harald Seeger (72128)
Tanja Fehm (23618)
Hans Neubauer (23624)

September 2018

Validation 5 FFPE samples analogue to FF samples, Description: A) Analogue samples FFPE-Cryo: The se...

Additional file 3: of Assessing breast cancer cell lines as tumour models by comparison of mRNA expression profiles

Krista Vincent (3576728)
Scott Findlay (3576725)
Lynne Postovit (3576731)

August 2015

Top 1 % of differentially expressed genes between tumours and cell lines after filtering out genes c...

Additional file 7: of Integrated proteotranscriptomics of breast cancer reveals globally increased protein-mRNA concordance associated with subtypes and survival

Wei Tang (53470)
Ming Zhou (73279)
Tiffany Dorsey (6036011)
DaRue Prieto (6036014)
Xin Wang (91924)
Eytan Ruppin (23002)
Timothy Veenstra (113151)
Stefan Ambs (37080)

December 2018

Tables S5. Significantly differentially expressed proteins between breast tumors and adjacent non-ca...

Additional file 3: of Classification of triple-negative breast cancers based on Immunogenomic profiling

Yin He (120155)
Zehang Jiang (6164414)
Cai Chen (181184)
Xiaosheng Wang (553236)

December 2018

Figure S2. Comparisons of the expression levels of immune-related genes between TNBC subtypes. A. Co...

Additional file 4: of Assessing breast cancer cell lines as tumour models by comparison of mRNA expression profiles

Krista Vincent (3576728)
Scott Findlay (3576725)
Lynne Postovit (3576731)

August 2015

Comparison of the frequency of select mutational events in breast cancer tumours versus cell lines. ...

Additional file 2: of Assessing breast cancer cell lines as tumour models by comparison of mRNA expression profiles

Krista Vincent (3576728)
Scott Findlay (3576725)
Lynne Postovit (3576731)

August 2015

Top 1 % of differentially expressed genes between tumours and cell lines (with adjusted p values by ...

Additional file 2: of Classification of triple-negative breast cancers based on Immunogenomic profiling

Yin He (120155)
Zehang Jiang (6164414)
Cai Chen (181184)
Xiaosheng Wang (553236)

December 2018

Figure S1. Comparisons of the stromal content and tumor purity between TNBC subtypes (MannâWhitney...

Additional file 3: of Molecular biomarkers screened by next-generation RNA sequencing for non-sentinel lymph node status prediction in breast cancer patients with metastatic sentinel lymph nodes

Feng Liang (447805)
Hongzhu Qu (36515)
Qiang Lin (208776)
Yadong Yang (396824)
Xiuyan Ruan (3450233)
Bo Zhang (6559)
Yi Liu (36759)
Chengze Yu (3450230)
Hongyan Zhang (618068)
Xiangdong Fang (180671)
Xiaopeng Hao (1644652)

August 2015

Scatter plots of gene expression values between samples. A figure illustrating how similar of genes ...

Additional file 3: of The association of genomic lesions and PD-1/PD-L1 expression in resected triple-negative breast cancers

Michael Barrett (128123)
Elizabeth Lenkiewicz (117033)
Smriti Malasi (5505893)
Anamika Basu (334844)
Jennifer Yearley (5505899)
Lakshmanan Annamalai (358396)
Ann McCullough (5505890)
Heidi Kosiorek (5505896)
Pooja Narang (298385)
Melissa Wilson Sayres (5505905)
Meixuan Chen (5505902)
Karen Anderson (217635)
Barbara Pockaj (117056)

July 2018

Figure S3. Flow-sorting fresh frozen (FF) TNBC tissue samples. DNA content analysis of diploid and a...

Additional file 1: of RNA-sequencing in non-small cell lung cancer shows gene downregulation of therapeutic targets in tumor tissue compared to non-malignant lung tissue

Kobe Reynders (5526461)
Els Wauters (101718)
Matthieu Moisse (659185)
Herbert DecaluwĂŠ (5526488)
Paul De Leyn (5526455)
StĂŠphanie Peeters (5526485)
Maarten Lambrecht (5526458)
Kristiaan Nackaerts (3210705)
Christophe Dooms (2938749)
Wim Janssens (101722)
Johan Vansteenkiste (5526467)
Diether Lambrechts (101772)
Dirk De Ruysscher (810406)

July 2018

Table S1. RNA-sequencing results for tumor tissue (a) or non-malignant lung tissue (b). Differential...

Additional file 7: of Separation of breast cancer and organ microenvironment transcriptomes in metastases

Mohammad Alzubi (6431630)
Tia Turner (6431633)
Amy Olex (6431636)
Sahib Sohal (6431639)
Nicholas Tobin (4848271)
Susana Recio (6431642)
Jonas Bergh (23551)
Thomas Hatschek (22685)
Joel Parker (17174)
Carol Sartorius (6431645)
Charles Perou (3530138)
Mikhail Dozmorov (4630)
J. Harrell (6413768)

March 2019

Genes upregulated during liver metastasis; cancer and organ-specific changes. DESeq2 was used to ide...

Additional file 7: of Identification of three subtypes of triple-negative breast cancer with potential therapeutic implications

Pascal Jézéquel (217021)
Olivier Kerdraon (6711944)
Hubert Hondermarck (3624869)
Catherine Guérin-Charbonnel (3399809)
Hamza Lasla (3399812)
Wilfried Gouraud (3399800)
Jean-Luc Canon (2587597)
Andrea Gombos (3147276)
Florence Dalenc (15454)
Suzette Delaloge (805610)
Jérôme Lemonnier (5845856)
Delphine Loussouarn (128055)
Véronique Verrièle (6711947)
Mario Campone (217018)

May 2019

Projection of internal TNBC cohort in the first PCA plane. (C1, n = 55 [blue]; C2, n = 98 [red]; C3,...

Additional file 7: of Comparison of triple-negative breast cancer molecular subtyping using RNA from matched fresh-frozen versus formalin-fixed paraffin-embedded tissue

Abstract

Extracted data

Additional file 7: of Comparison of triple-negative breast cancer molecular subtyping using RNA from matched fresh-frozen versus formalin-fixed paraffin-embedded tissue

Abstract

Extracted data

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