Landscape of Bone Marrow Metastasis in Human Neuroblastoma Unraveled by Transcriptomics and Deep Multiplex Imaging

Lazic, Daria
Kromp, Florian
Rifatbegovic, Fikret
Repiscak, Peter
Kirr, Michael
Mivalt, Filip
Halbritter, Florian
Bernkopf, Marie
Bileck, Andrea
Marek, Ussowicz
Ambros, Inge M.
Ambros, Peter F.
Gerner, Christopher
Ladenstein, Ruth
Ostalecki, Christian
Taschner-Mandl, Sabine

Publication date

August 2021

DOI

Abstract

MELC (Multi-epitope ligand cartography) multiplex imaging data of our neuroblastoma cohort supporting the publication " Landscape of Bone Marrow Metastasis in Human Neuroblastoma Unraveled by Transcriptomics and Deep Multiplex Imaging". The zip folders contain raw image data of one to four fields of view (FoV). The folder "RoI" contains the masks of user-selected regions. "marker_status.csv" is used for normalization with RESTORE. "MELC_single_cell_data.csv" contains the normalized single-cell data with cell type assignments

Extracted data

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Data Protection

Landscape of Bone Marrow Metastasis in Human Neuroblastoma Unraveled by Transcriptomics and Deep Multiplex Imaging

Lazic, Daria
Kromp, Florian
Rifatbegovic, Fikret
Repiscak, Peter
Kirr, Michael
Mivalt, Filip
Halbritter, Florian
Bernkopf, Marie
Bileck, Andrea
Marek, Ussowicz
Ambros, Inge M.
Ambros, Peter F.
Gerner, Christopher
Ladenstein, Ruth
Ostalecki, Christian
Taschner-Mandl, Sabine

Open link

Publication date

August 2021

DOI

10.5281/zenodo.6621045

Abstract

Extracted data

Brouwer, Nelleke P.M.
Webbink, Loth
Haddad, Tariq S.
Rutgers, Natasja
Van Vliet, Shannon
Wood, Colin S.
Jansen, Pascal W.T.C.
imCMS consortium
De Wilt, Johannes H.W.
Hugen, Niek
Simmer, Femke
Jamieson, Nigel B.
Tauriello, Daniele V.F.
Vermeulen, Michiel
Nagtegaal, Iris D.

April 2023

Spatial transcriptomic data (counts_DSP_afterQC_normalisation.csv) derived using the Nanostring GeoM...

Isolation of disseminated neuroblastoma cells from bone marrow aspirates for pretreatment risk assessment by array comparative genomic hybridization

Vandewoestyne, Mado
Kumps, Candy
Swerts, Katrien
Menten, Björn
Lammens, Tim
Philippé, Jan
De Preter, Katleen
Laureys, Genevieve
Van Roy, Nadine
Speleman, Franki
Deforce, Dieter

January 2012

In neuroblastoma, tumor biopsies are used for prognostic evaluation and risk assessment by molecular...

Landscape of Bone Marrow Metastasis in Human Neuroblastoma Unraveled by Transcriptomics and Deep Multiplex Imaging

Lazic, Daria
Kromp, Florian
Rifatbegovic, Fikret
Repiscak, Peter
Kirr, Michael
Mivalt, Filip
Halbritter, Florian
Bernkopf, Marie
Bileck, Andrea
Marek, Ussowicz
Ambros, Inge M.
Ambros, Peter F.
Gerner, Christopher
Ladenstein, Ruth
Ostalecki, Christian
Taschner-Mandl, Sabine

August 2021

MELC (Multi-epitope ligand cartography) multiplex imaging data of our neuroblastoma cohort supportin...

Supporting data for "Dissecting the cellular architecture of neuroblastoma bone marrow metastasis using single-cell transcriptomics and epigenomics unravels the role of monocytes at the metastatic niche"

Fetahu, Irfete S.
Esser-Skala, Wolfgang
Dnyansagar, Rohit
Sindelar, Samuel
Rifatbegovic, Fikret
Bileck, Andrea
Skos, Lukas
Bozsaky, Eva
Lazic, Daria
Shaw, Lisa
Tötzl, Marcus
Tarlungeanu, Dora
Bernkopf, Marie
Rados, Magdalena
Weninger, Wolfgang
Tomazou, Eleni M.
Bock, Christoph
Gerner, Christopher
Ladenstein, Ruth
Farlik, Matthias
Fortelny, Nikolaus
Taschner-Mandl, Sabine

June 2023

This data repository contains several datasets supplementing the paper “Dissecting the cellular arch...

Image_1_Pro-metastatic and mesenchymal gene expression signatures characterize circulating tumor cells of neuroblastoma patients with bone marrow metastases and relapse.tif

Amos H. P. Loh (11562304)
Clara Angelina (13776805)
Meng Kang Wong (11562286)
Sheng Hui Tan (11562289)
Sarvesh A. Sukhatme (13776808)
Trifanny Yeo (5071130)
Su Bin Lim (13776811)
York Tien Lee (13776814)
Shui Yen Soh (11562301)
Wing Leung (3563864)
Kenneth T. E. Chang (8976572)
Yong Wei Chua (7429961)
Syed M. F. Alkaff (13776817)
Tony K. H. Lim (13776820)
Chwee Teck Lim (217031)
Zhi Xiong Chen (9248660)

September 2022

Existing marker-based methods of minimal residual disease (MRD) determination in neuroblastoma do no...

Image_3_Pro-metastatic and mesenchymal gene expression signatures characterize circulating tumor cells of neuroblastoma patients with bone marrow metastases and relapse.tif

Amos H. P. Loh (11562304)
Clara Angelina (13776805)
Meng Kang Wong (11562286)
Sheng Hui Tan (11562289)
Sarvesh A. Sukhatme (13776808)
Trifanny Yeo (5071130)
Su Bin Lim (13776811)
York Tien Lee (13776814)
Shui Yen Soh (11562301)
Wing Leung (3563864)
Kenneth T. E. Chang (8976572)
Yong Wei Chua (7429961)
Syed M. F. Alkaff (13776817)
Tony K. H. Lim (13776820)
Chwee Teck Lim (217031)
Zhi Xiong Chen (9248660)

September 2022

Existing marker-based methods of minimal residual disease (MRD) determination in neuroblastoma do no...

Image_4_Pro-metastatic and mesenchymal gene expression signatures characterize circulating tumor cells of neuroblastoma patients with bone marrow metastases and relapse.tif

Amos H. P. Loh (11562304)
Clara Angelina (13776805)
Meng Kang Wong (11562286)
Sheng Hui Tan (11562289)
Sarvesh A. Sukhatme (13776808)
Trifanny Yeo (5071130)
Su Bin Lim (13776811)
York Tien Lee (13776814)
Shui Yen Soh (11562301)
Wing Leung (3563864)
Kenneth T. E. Chang (8976572)
Yong Wei Chua (7429961)
Syed M. F. Alkaff (13776817)
Tony K. H. Lim (13776820)
Chwee Teck Lim (217031)
Zhi Xiong Chen (9248660)

September 2022

Existing marker-based methods of minimal residual disease (MRD) determination in neuroblastoma do no...

Image_2_Pro-metastatic and mesenchymal gene expression signatures characterize circulating tumor cells of neuroblastoma patients with bone marrow metastases and relapse.tif

Amos H. P. Loh (11562304)
Clara Angelina (13776805)
Meng Kang Wong (11562286)
Sheng Hui Tan (11562289)
Sarvesh A. Sukhatme (13776808)
Trifanny Yeo (5071130)
Su Bin Lim (13776811)
York Tien Lee (13776814)
Shui Yen Soh (11562301)
Wing Leung (3563864)
Kenneth T. E. Chang (8976572)
Yong Wei Chua (7429961)
Syed M. F. Alkaff (13776817)
Tony K. H. Lim (13776820)
Chwee Teck Lim (217031)
Zhi Xiong Chen (9248660)

September 2022

Existing marker-based methods of minimal residual disease (MRD) determination in neuroblastoma do no...

DataSheet_3_Pro-metastatic and mesenchymal gene expression signatures characterize circulating tumor cells of neuroblastoma patients with bone marrow metastases and relapse.xlsx

Amos H. P. Loh (11562304)
Clara Angelina (13776805)
Meng Kang Wong (11562286)
Sheng Hui Tan (11562289)
Sarvesh A. Sukhatme (13776808)
Trifanny Yeo (5071130)
Su Bin Lim (13776811)
York Tien Lee (13776814)
Shui Yen Soh (11562301)
Wing Leung (3563864)
Kenneth T. E. Chang (8976572)
Yong Wei Chua (7429961)
Syed M. F. Alkaff (13776817)
Tony K. H. Lim (13776820)
Chwee Teck Lim (217031)
Zhi Xiong Chen (9248660)

September 2022

Existing marker-based methods of minimal residual disease (MRD) determination in neuroblastoma do no...

DataSheet_1_Pro-metastatic and mesenchymal gene expression signatures characterize circulating tumor cells of neuroblastoma patients with bone marrow metastases and relapse.xlsx

Amos H. P. Loh (11562304)
Clara Angelina (13776805)
Meng Kang Wong (11562286)
Sheng Hui Tan (11562289)
Sarvesh A. Sukhatme (13776808)
Trifanny Yeo (5071130)
Su Bin Lim (13776811)
York Tien Lee (13776814)
Shui Yen Soh (11562301)
Wing Leung (3563864)
Kenneth T. E. Chang (8976572)
Yong Wei Chua (7429961)
Syed M. F. Alkaff (13776817)
Tony K. H. Lim (13776820)
Chwee Teck Lim (217031)
Zhi Xiong Chen (9248660)

September 2022

Existing marker-based methods of minimal residual disease (MRD) determination in neuroblastoma do no...

Table_1_Pro-metastatic and mesenchymal gene expression signatures characterize circulating tumor cells of neuroblastoma patients with bone marrow metastases and relapse.docx

Amos H. P. Loh (11562304)
Clara Angelina (13776805)
Meng Kang Wong (11562286)
Sheng Hui Tan (11562289)
Sarvesh A. Sukhatme (13776808)
Trifanny Yeo (5071130)
Su Bin Lim (13776811)
York Tien Lee (13776814)
Shui Yen Soh (11562301)
Wing Leung (3563864)
Kenneth T. E. Chang (8976572)
Yong Wei Chua (7429961)
Syed M. F. Alkaff (13776817)
Tony K. H. Lim (13776820)
Chwee Teck Lim (217031)
Zhi Xiong Chen (9248660)

September 2022

Existing marker-based methods of minimal residual disease (MRD) determination in neuroblastoma do no...

DataSheet_4_Pro-metastatic and mesenchymal gene expression signatures characterize circulating tumor cells of neuroblastoma patients with bone marrow metastases and relapse.xlsx

Amos H. P. Loh (11562304)
Clara Angelina (13776805)
Meng Kang Wong (11562286)
Sheng Hui Tan (11562289)
Sarvesh A. Sukhatme (13776808)
Trifanny Yeo (5071130)
Su Bin Lim (13776811)
York Tien Lee (13776814)
Shui Yen Soh (11562301)
Wing Leung (3563864)
Kenneth T. E. Chang (8976572)
Yong Wei Chua (7429961)
Syed M. F. Alkaff (13776817)
Tony K. H. Lim (13776820)
Chwee Teck Lim (217031)
Zhi Xiong Chen (9248660)

September 2022

Existing marker-based methods of minimal residual disease (MRD) determination in neuroblastoma do no...

DataSheet_2_Pro-metastatic and mesenchymal gene expression signatures characterize circulating tumor cells of neuroblastoma patients with bone marrow metastases and relapse.xlsx

Amos H. P. Loh (11562304)
Clara Angelina (13776805)
Meng Kang Wong (11562286)
Sheng Hui Tan (11562289)
Sarvesh A. Sukhatme (13776808)
Trifanny Yeo (5071130)
Su Bin Lim (13776811)
York Tien Lee (13776814)
Shui Yen Soh (11562301)
Wing Leung (3563864)
Kenneth T. E. Chang (8976572)
Yong Wei Chua (7429961)
Syed M. F. Alkaff (13776817)
Tony K. H. Lim (13776820)
Chwee Teck Lim (217031)
Zhi Xiong Chen (9248660)

September 2022

Existing marker-based methods of minimal residual disease (MRD) determination in neuroblastoma do no...

Transcriptomics and proteomics reveal distinct biology for lymph node metastases and tumor deposits in colorectal cancer

Brouwer, Nelleke P.M.
Webbink, Loth
Haddad, Tariq S.
Rutgers, Natasja
Van Vliet, Shannon
Wood, Colin S.
Jansen, Pascal W.T.C.
imCMS consortium
De Wilt, Johannes H.W.
Hugen, Niek
Simmer, Femke
Jamieson, Nigel B.
Tauriello, Daniele V.F.
Vermeulen, Michiel
Nagtegaal, Iris D.

April 2023

Spatial transcriptomic data (counts_DSP_afterQC_normalisation.csv) derived using the Nanostring GeoM...

Isolation of disseminated neuroblastoma cells from bone marrow aspirates for pretreatment risk assessment by array comparative genomic hybridization

Vandewoestyne, Mado
Kumps, Candy
Swerts, Katrien
Menten, Björn
Lammens, Tim
Philippé, Jan
De Preter, Katleen
Laureys, Genevieve
Van Roy, Nadine
Speleman, Franki
Deforce, Dieter

January 2012

In neuroblastoma, tumor biopsies are used for prognostic evaluation and risk assessment by molecular...

Landscape of Bone Marrow Metastasis in Human Neuroblastoma Unraveled by Transcriptomics and Deep Multiplex Imaging

Lazic, Daria
Kromp, Florian
Rifatbegovic, Fikret
Repiscak, Peter
Kirr, Michael
Mivalt, Filip
Halbritter, Florian
Bernkopf, Marie
Bileck, Andrea
Marek, Ussowicz
Ambros, Inge M.
Ambros, Peter F.
Gerner, Christopher
Ladenstein, Ruth
Ostalecki, Christian
Taschner-Mandl, Sabine

August 2021

MELC (Multi-epitope ligand cartography) multiplex imaging data of our neuroblastoma cohort supportin...

Fetahu, Irfete S.
Esser-Skala, Wolfgang
Dnyansagar, Rohit
Sindelar, Samuel
Rifatbegovic, Fikret
Bileck, Andrea
Skos, Lukas
Bozsaky, Eva
Lazic, Daria
Shaw, Lisa
Tötzl, Marcus
Tarlungeanu, Dora
Bernkopf, Marie
Rados, Magdalena
Weninger, Wolfgang
Tomazou, Eleni M.
Bock, Christoph
Gerner, Christopher
Ladenstein, Ruth
Farlik, Matthias
Fortelny, Nikolaus
Taschner-Mandl, Sabine

June 2023

This data repository contains several datasets supplementing the paper “Dissecting the cellular arch...

Image_1_Pro-metastatic and mesenchymal gene expression signatures characterize circulating tumor cells of neuroblastoma patients with bone marrow metastases and relapse.tif

Amos H. P. Loh (11562304)
Clara Angelina (13776805)
Meng Kang Wong (11562286)
Sheng Hui Tan (11562289)
Sarvesh A. Sukhatme (13776808)
Trifanny Yeo (5071130)
Su Bin Lim (13776811)
York Tien Lee (13776814)
Shui Yen Soh (11562301)
Wing Leung (3563864)
Kenneth T. E. Chang (8976572)
Yong Wei Chua (7429961)
Syed M. F. Alkaff (13776817)
Tony K. H. Lim (13776820)
Chwee Teck Lim (217031)
Zhi Xiong Chen (9248660)

September 2022

Existing marker-based methods of minimal residual disease (MRD) determination in neuroblastoma do no...

Image_3_Pro-metastatic and mesenchymal gene expression signatures characterize circulating tumor cells of neuroblastoma patients with bone marrow metastases and relapse.tif

Amos H. P. Loh (11562304)
Clara Angelina (13776805)
Meng Kang Wong (11562286)
Sheng Hui Tan (11562289)
Sarvesh A. Sukhatme (13776808)
Trifanny Yeo (5071130)
Su Bin Lim (13776811)
York Tien Lee (13776814)
Shui Yen Soh (11562301)
Wing Leung (3563864)
Kenneth T. E. Chang (8976572)
Yong Wei Chua (7429961)
Syed M. F. Alkaff (13776817)
Tony K. H. Lim (13776820)
Chwee Teck Lim (217031)
Zhi Xiong Chen (9248660)

September 2022

Existing marker-based methods of minimal residual disease (MRD) determination in neuroblastoma do no...

Image_4_Pro-metastatic and mesenchymal gene expression signatures characterize circulating tumor cells of neuroblastoma patients with bone marrow metastases and relapse.tif

Amos H. P. Loh (11562304)
Clara Angelina (13776805)
Meng Kang Wong (11562286)
Sheng Hui Tan (11562289)
Sarvesh A. Sukhatme (13776808)
Trifanny Yeo (5071130)
Su Bin Lim (13776811)
York Tien Lee (13776814)
Shui Yen Soh (11562301)
Wing Leung (3563864)
Kenneth T. E. Chang (8976572)
Yong Wei Chua (7429961)
Syed M. F. Alkaff (13776817)
Tony K. H. Lim (13776820)
Chwee Teck Lim (217031)
Zhi Xiong Chen (9248660)

September 2022

Existing marker-based methods of minimal residual disease (MRD) determination in neuroblastoma do no...

Image_2_Pro-metastatic and mesenchymal gene expression signatures characterize circulating tumor cells of neuroblastoma patients with bone marrow metastases and relapse.tif

Amos H. P. Loh (11562304)
Clara Angelina (13776805)
Meng Kang Wong (11562286)
Sheng Hui Tan (11562289)
Sarvesh A. Sukhatme (13776808)
Trifanny Yeo (5071130)
Su Bin Lim (13776811)
York Tien Lee (13776814)
Shui Yen Soh (11562301)
Wing Leung (3563864)
Kenneth T. E. Chang (8976572)
Yong Wei Chua (7429961)
Syed M. F. Alkaff (13776817)
Tony K. H. Lim (13776820)
Chwee Teck Lim (217031)
Zhi Xiong Chen (9248660)

September 2022

Existing marker-based methods of minimal residual disease (MRD) determination in neuroblastoma do no...

DataSheet_3_Pro-metastatic and mesenchymal gene expression signatures characterize circulating tumor cells of neuroblastoma patients with bone marrow metastases and relapse.xlsx

Amos H. P. Loh (11562304)
Clara Angelina (13776805)
Meng Kang Wong (11562286)
Sheng Hui Tan (11562289)
Sarvesh A. Sukhatme (13776808)
Trifanny Yeo (5071130)
Su Bin Lim (13776811)
York Tien Lee (13776814)
Shui Yen Soh (11562301)
Wing Leung (3563864)
Kenneth T. E. Chang (8976572)
Yong Wei Chua (7429961)
Syed M. F. Alkaff (13776817)
Tony K. H. Lim (13776820)
Chwee Teck Lim (217031)
Zhi Xiong Chen (9248660)

September 2022

Existing marker-based methods of minimal residual disease (MRD) determination in neuroblastoma do no...

DataSheet_1_Pro-metastatic and mesenchymal gene expression signatures characterize circulating tumor cells of neuroblastoma patients with bone marrow metastases and relapse.xlsx

Amos H. P. Loh (11562304)
Clara Angelina (13776805)
Meng Kang Wong (11562286)
Sheng Hui Tan (11562289)
Sarvesh A. Sukhatme (13776808)
Trifanny Yeo (5071130)
Su Bin Lim (13776811)
York Tien Lee (13776814)
Shui Yen Soh (11562301)
Wing Leung (3563864)
Kenneth T. E. Chang (8976572)
Yong Wei Chua (7429961)
Syed M. F. Alkaff (13776817)
Tony K. H. Lim (13776820)
Chwee Teck Lim (217031)
Zhi Xiong Chen (9248660)

September 2022

Existing marker-based methods of minimal residual disease (MRD) determination in neuroblastoma do no...

Table_1_Pro-metastatic and mesenchymal gene expression signatures characterize circulating tumor cells of neuroblastoma patients with bone marrow metastases and relapse.docx

Amos H. P. Loh (11562304)
Clara Angelina (13776805)
Meng Kang Wong (11562286)
Sheng Hui Tan (11562289)
Sarvesh A. Sukhatme (13776808)
Trifanny Yeo (5071130)
Su Bin Lim (13776811)
York Tien Lee (13776814)
Shui Yen Soh (11562301)
Wing Leung (3563864)
Kenneth T. E. Chang (8976572)
Yong Wei Chua (7429961)
Syed M. F. Alkaff (13776817)
Tony K. H. Lim (13776820)
Chwee Teck Lim (217031)
Zhi Xiong Chen (9248660)

September 2022

Existing marker-based methods of minimal residual disease (MRD) determination in neuroblastoma do no...

DataSheet_4_Pro-metastatic and mesenchymal gene expression signatures characterize circulating tumor cells of neuroblastoma patients with bone marrow metastases and relapse.xlsx

Amos H. P. Loh (11562304)
Clara Angelina (13776805)
Meng Kang Wong (11562286)
Sheng Hui Tan (11562289)
Sarvesh A. Sukhatme (13776808)
Trifanny Yeo (5071130)
Su Bin Lim (13776811)
York Tien Lee (13776814)
Shui Yen Soh (11562301)
Wing Leung (3563864)
Kenneth T. E. Chang (8976572)
Yong Wei Chua (7429961)
Syed M. F. Alkaff (13776817)
Tony K. H. Lim (13776820)
Chwee Teck Lim (217031)
Zhi Xiong Chen (9248660)

September 2022

Existing marker-based methods of minimal residual disease (MRD) determination in neuroblastoma do no...

DataSheet_2_Pro-metastatic and mesenchymal gene expression signatures characterize circulating tumor cells of neuroblastoma patients with bone marrow metastases and relapse.xlsx

Amos H. P. Loh (11562304)
Clara Angelina (13776805)
Meng Kang Wong (11562286)
Sheng Hui Tan (11562289)
Sarvesh A. Sukhatme (13776808)
Trifanny Yeo (5071130)
Su Bin Lim (13776811)
York Tien Lee (13776814)
Shui Yen Soh (11562301)
Wing Leung (3563864)
Kenneth T. E. Chang (8976572)
Yong Wei Chua (7429961)
Syed M. F. Alkaff (13776817)
Tony K. H. Lim (13776820)
Chwee Teck Lim (217031)
Zhi Xiong Chen (9248660)

September 2022

Existing marker-based methods of minimal residual disease (MRD) determination in neuroblastoma do no...

Transcriptomics and proteomics reveal distinct biology for lymph node metastases and tumor deposits in colorectal cancer

Brouwer, Nelleke P.M.
Webbink, Loth
Haddad, Tariq S.
Rutgers, Natasja
Van Vliet, Shannon
Wood, Colin S.
Jansen, Pascal W.T.C.
imCMS consortium
De Wilt, Johannes H.W.
Hugen, Niek
Simmer, Femke
Jamieson, Nigel B.
Tauriello, Daniele V.F.
Vermeulen, Michiel
Nagtegaal, Iris D.

April 2023

Spatial transcriptomic data (counts_DSP_afterQC_normalisation.csv) derived using the Nanostring GeoM...

Isolation of disseminated neuroblastoma cells from bone marrow aspirates for pretreatment risk assessment by array comparative genomic hybridization

Vandewoestyne, Mado
Kumps, Candy
Swerts, Katrien
Menten, Björn
Lammens, Tim
Philippé, Jan
De Preter, Katleen
Laureys, Genevieve
Van Roy, Nadine
Speleman, Franki
Deforce, Dieter

January 2012

In neuroblastoma, tumor biopsies are used for prognostic evaluation and risk assessment by molecular...

Landscape of Bone Marrow Metastasis in Human Neuroblastoma Unraveled by Transcriptomics and Deep Multiplex Imaging

Abstract

Extracted data

Landscape of Bone Marrow Metastasis in Human Neuroblastoma Unraveled by Transcriptomics and Deep Multiplex Imaging

Abstract

Extracted data

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