Which dataset
would you like to
analyze in BBrowser?

Species: human
Number of cells: 147137
Number of downloads: 24
Study size: 4GB
Uploaded at:

Immunology 
immuno-oncology 
Human Cell Atlas 
lung adenocarcinoma 
Cancer 
Small cell lung cancer 
Non-small cell lung cancer 

Signatures of plasticity, metastasis, and immunosuppression in an atlas of human small cell lung cancer (All cells)

Joseph M. Chan, Álvaro Quintanal-Villalonga, Vianne Ran Gao, Yubin Xie, Viola Allaj, Ojasvi Chaudhary, Ignas Masilionis, Jacklynn Egger, Andrew Chow, Thomas Walle, Marissa Mattar, Dig V.K. Yarlagadda, James L. Wang, Fathema Uddin, Michael Offin, Metamia Ciampricotti, Besnik Qeriqi, Amber Bahr, Elisa de Stanchina, Umesh K. Bhanot, W. Victoria Lai, Matthew J. Bott, David R. Jones, Arvin Ruiz, Marina K. Baine, Yanyun Li, Natasha Rekhtman, John T. Poirier, Tal Nawy, Triparna Sen, Linas Mazutis, Travis J. Hollmann, Dana Pe'er, Charles M. Rudin

Small cell lung cancer (SCLC) is an aggressive malignancy that includes subtypes defined by differential expression of ASCL1, NEUROD1, and POU2F3 (SCLC-A, -N, and -P, respectively). To define the heterogeneity of tumors and their associated microenvironments across subtypes, we sequenced 155,098 transcriptomes from 21 human biospecimens, including 54,523 SCLC transcriptomes. We observe greater tumor diversity in SCLC than lung adenocarcinoma, driven by canonical, intermediate, and admixed subtypes. We discover a PLCG2-high SCLC phenotype with stem-like, pro-metastatic features that recurs across subtypes and predicts worse overall survival. SCLC exhibits greater immune sequestration and less immune infiltration than lung adenocarcinoma, and SCLC-N shows less immune infiltrate and greater T cell dysfunction than SCLC-A. We identify a profibrotic, immunosuppressive monocyte/macrophage population in SCLC tumors that is particularly associated with the recurrent, PLCG2-high subpopulation.

Download bbrowser to analyze now

Species: human
Number of cells: 64091
Number of downloads: 12
Study size: 2GB
Uploaded at:

Immunology 
immuno-oncology 
Human Cell Atlas 
lung adenocarcinoma 
Cancer 
Small cell lung cancer 
Non-small cell lung cancer 

Signatures of plasticity, metastasis, and immunosuppression in an atlas of human small cell lung cancer (Epithelial cells)

Joseph M. Chan, Álvaro Quintanal-Villalonga, Vianne Ran Gao, Yubin Xie, Viola Allaj, Ojasvi Chaudhary, Ignas Masilionis, Jacklynn Egger, Andrew Chow, Thomas Walle, Marissa Mattar, Dig V.K. Yarlagadda, James L. Wang, Fathema Uddin, Michael Offin, Metamia Ciampricotti, Besnik Qeriqi, Amber Bahr, Elisa de Stanchina, Umesh K. Bhanot, W. Victoria Lai, Matthew J. Bott, David R. Jones, Arvin Ruiz, Marina K. Baine, Yanyun Li, Natasha Rekhtman, John T. Poirier, Tal Nawy, Triparna Sen, Linas Mazutis, Travis J. Hollmann, Dana Pe'er, Charles M. Rudin

Small cell lung cancer (SCLC) is an aggressive malignancy that includes subtypes defined by differential expression of ASCL1, NEUROD1, and POU2F3 (SCLC-A, -N, and -P, respectively). To define the heterogeneity of tumors and their associated microenvironments across subtypes, we sequenced 155,098 transcriptomes from 21 human biospecimens, including 54,523 SCLC transcriptomes. We observe greater tumor diversity in SCLC than lung adenocarcinoma, driven by canonical, intermediate, and admixed subtypes. We discover a PLCG2-high SCLC phenotype with stem-like, pro-metastatic features that recurs across subtypes and predicts worse overall survival. SCLC exhibits greater immune sequestration and less immune infiltration than lung adenocarcinoma, and SCLC-N shows less immune infiltrate and greater T cell dysfunction than SCLC-A. We identify a profibrotic, immunosuppressive monocyte/macrophage population in SCLC tumors that is particularly associated with the recurrent, PLCG2-high subpopulation.

Download bbrowser to analyze now

Species: human
Number of cells: 54313
Number of downloads: 5
Study size: 2GB
Uploaded at:

Immunology 
immuno-oncology 
Human Cell Atlas 
lung adenocarcinoma 
Cancer 
Small cell lung cancer 
Non-small cell lung cancer 

Signatures of plasticity, metastasis, and immunosuppression in an atlas of human small cell lung cancer (SCLC tumor cells)

Joseph M. Chan, Álvaro Quintanal-Villalonga, Vianne Ran Gao, Yubin Xie, Viola Allaj, Ojasvi Chaudhary, Ignas Masilionis, Jacklynn Egger, Andrew Chow, Thomas Walle, Marissa Mattar, Dig V.K. Yarlagadda, James L. Wang, Fathema Uddin, Michael Offin, Metamia Ciampricotti, Besnik Qeriqi, Amber Bahr, Elisa de Stanchina, Umesh K. Bhanot, W. Victoria Lai, Matthew J. Bott, David R. Jones, Arvin Ruiz, Marina K. Baine, Yanyun Li, Natasha Rekhtman, John T. Poirier, Tal Nawy, Triparna Sen, Linas Mazutis, Travis J. Hollmann, Dana Pe'er, Charles M. Rudin

Small cell lung cancer (SCLC) is an aggressive malignancy that includes subtypes defined by differential expression of ASCL1, NEUROD1, and POU2F3 (SCLC-A, -N, and -P, respectively). To define the heterogeneity of tumors and their associated microenvironments across subtypes, we sequenced 155,098 transcriptomes from 21 human biospecimens, including 54,523 SCLC transcriptomes. We observe greater tumor diversity in SCLC than lung adenocarcinoma, driven by canonical, intermediate, and admixed subtypes. We discover a PLCG2-high SCLC phenotype with stem-like, pro-metastatic features that recurs across subtypes and predicts worse overall survival. SCLC exhibits greater immune sequestration and less immune infiltration than lung adenocarcinoma, and SCLC-N shows less immune infiltrate and greater T cell dysfunction than SCLC-A. We identify a profibrotic, immunosuppressive monocyte/macrophage population in SCLC tumors that is particularly associated with the recurrent, PLCG2-high subpopulation.

Download bbrowser to analyze now

Species: human
Number of cells: 16475
Number of downloads: 11
Study size: 278MB
Uploaded at:

Immunology 
immuno-oncology 
Human Cell Atlas 
lung adenocarcinoma 
Cancer 
Small cell lung cancer 
Non-small cell lung cancer 

Signatures of plasticity, metastasis, and immunosuppression in an atlas of human small cell lung cancer (SCLC immune cells)

Joseph M. Chan, Álvaro Quintanal-Villalonga, Vianne Ran Gao, Yubin Xie, Viola Allaj, Ojasvi Chaudhary, Ignas Masilionis, Jacklynn Egger, Andrew Chow, Thomas Walle, Marissa Mattar, Dig V.K. Yarlagadda, James L. Wang, Fathema Uddin, Michael Offin, Metamia Ciampricotti, Besnik Qeriqi, Amber Bahr, Elisa de Stanchina, Umesh K. Bhanot, W. Victoria Lai, Matthew J. Bott, David R. Jones, Arvin Ruiz, Marina K. Baine, Yanyun Li, Natasha Rekhtman, John T. Poirier, Tal Nawy, Triparna Sen, Linas Mazutis, Travis J. Hollmann, Dana Pe'er, Charles M. Rudin

Small cell lung cancer (SCLC) is an aggressive malignancy that includes subtypes defined by differential expression of ASCL1, NEUROD1, and POU2F3 (SCLC-A, -N, and -P, respectively). To define the heterogeneity of tumors and their associated microenvironments across subtypes, we sequenced 155,098 transcriptomes from 21 human biospecimens, including 54,523 SCLC transcriptomes. We observe greater tumor diversity in SCLC than lung adenocarcinoma, driven by canonical, intermediate, and admixed subtypes. We discover a PLCG2-high SCLC phenotype with stem-like, pro-metastatic features that recurs across subtypes and predicts worse overall survival. SCLC exhibits greater immune sequestration and less immune infiltration than lung adenocarcinoma, and SCLC-N shows less immune infiltrate and greater T cell dysfunction than SCLC-A. We identify a profibrotic, immunosuppressive monocyte/macrophage population in SCLC tumors that is particularly associated with the recurrent, PLCG2-high subpopulation.

Download bbrowser to analyze now

Species: human
Number of cells: 2951
Number of downloads: 6
Study size: 47MB
Uploaded at:

Immunology 
immuno-oncology 
Human Cell Atlas 
lung adenocarcinoma 
Cancer 
Small cell lung cancer 
Non-small cell lung cancer 

Signatures of plasticity, metastasis, and immunosuppression in an atlas of human small cell lung cancer (SCLC myeloid)

Joseph M. Chan, Álvaro Quintanal-Villalonga, Vianne Ran Gao, Yubin Xie, Viola Allaj, Ojasvi Chaudhary, Ignas Masilionis, Jacklynn Egger, Andrew Chow, Thomas Walle, Marissa Mattar, Dig V.K. Yarlagadda, James L. Wang, Fathema Uddin, Michael Offin, Metamia Ciampricotti, Besnik Qeriqi, Amber Bahr, Elisa de Stanchina, Umesh K. Bhanot, W. Victoria Lai, Matthew J. Bott, David R. Jones, Arvin Ruiz, Marina K. Baine, Yanyun Li, Natasha Rekhtman, John T. Poirier, Tal Nawy, Triparna Sen, Linas Mazutis, Travis J. Hollmann, Dana Pe'er, Charles M. Rudin

Small cell lung cancer (SCLC) is an aggressive malignancy that includes subtypes defined by differential expression of ASCL1, NEUROD1, and POU2F3 (SCLC-A, -N, and -P, respectively). To define the heterogeneity of tumors and their associated microenvironments across subtypes, we sequenced 155,098 transcriptomes from 21 human biospecimens, including 54,523 SCLC transcriptomes. We observe greater tumor diversity in SCLC than lung adenocarcinoma, driven by canonical, intermediate, and admixed subtypes. We discover a PLCG2-high SCLC phenotype with stem-like, pro-metastatic features that recurs across subtypes and predicts worse overall survival. SCLC exhibits greater immune sequestration and less immune infiltration than lung adenocarcinoma, and SCLC-N shows less immune infiltrate and greater T cell dysfunction than SCLC-A. We identify a profibrotic, immunosuppressive monocyte/macrophage population in SCLC tumors that is particularly associated with the recurrent, PLCG2-high subpopulation.

Download bbrowser to analyze now

Species: human
Number of cells: 3923
Number of downloads: 4
Study size: 170MB
Uploaded at:

Immunology 
immuno-oncology 
Human Cell Atlas 
lung adenocarcinoma 
Cancer 
Small cell lung cancer 
Non-small cell lung cancer 

Signatures of plasticity, metastasis, and immunosuppression in an atlas of human small cell lung cancer (Sample RU1215)

Joseph M. Chan, Álvaro Quintanal-Villalonga, Vianne Ran Gao, Yubin Xie, Viola Allaj, Ojasvi Chaudhary, Ignas Masilionis, Jacklynn Egger, Andrew Chow, Thomas Walle, Marissa Mattar, Dig V.K. Yarlagadda, James L. Wang, Fathema Uddin, Michael Offin, Metamia Ciampricotti, Besnik Qeriqi, Amber Bahr, Elisa de Stanchina, Umesh K. Bhanot, W. Victoria Lai, Matthew J. Bott, David R. Jones, Arvin Ruiz, Marina K. Baine, Yanyun Li, Natasha Rekhtman, John T. Poirier, Tal Nawy, Triparna Sen, Linas Mazutis, Travis J. Hollmann, Dana Pe'er, Charles M. Rudin

Small cell lung cancer (SCLC) is an aggressive malignancy that includes subtypes defined by differential expression of ASCL1, NEUROD1, and POU2F3 (SCLC-A, -N, and -P, respectively). To define the heterogeneity of tumors and their associated microenvironments across subtypes, we sequenced 155,098 transcriptomes from 21 human biospecimens, including 54,523 SCLC transcriptomes. We observe greater tumor diversity in SCLC than lung adenocarcinoma, driven by canonical, intermediate, and admixed subtypes. We discover a PLCG2-high SCLC phenotype with stem-like, pro-metastatic features that recurs across subtypes and predicts worse overall survival. SCLC exhibits greater immune sequestration and less immune infiltration than lung adenocarcinoma, and SCLC-N shows less immune infiltrate and greater T cell dysfunction than SCLC-A. We identify a profibrotic, immunosuppressive monocyte/macrophage population in SCLC tumors that is particularly associated with the recurrent, PLCG2-high subpopulation.

Download bbrowser to analyze now

Species: human
Number of cells: 73047
Number of downloads: 5
Study size: 1GB
Uploaded at:

Immunology 
immuno-oncology 
Human Cell Atlas 
lung adenocarcinoma 
Cancer 
Small cell lung cancer 
Non-small cell lung cancer 

Signatures of plasticity, metastasis, and immunosuppression in an atlas of human small cell lung cancer (Combined immune cells)

Joseph M. Chan, Álvaro Quintanal-Villalonga, Vianne Ran Gao, Yubin Xie, Viola Allaj, Ojasvi Chaudhary, Ignas Masilionis, Jacklynn Egger, Andrew Chow, Thomas Walle, Marissa Mattar, Dig V.K. Yarlagadda, James L. Wang, Fathema Uddin, Michael Offin, Metamia Ciampricotti, Besnik Qeriqi, Amber Bahr, Elisa de Stanchina, Umesh K. Bhanot, W. Victoria Lai, Matthew J. Bott, David R. Jones, Arvin Ruiz, Marina K. Baine, Yanyun Li, Natasha Rekhtman, John T. Poirier, Tal Nawy, Triparna Sen, Linas Mazutis, Travis J. Hollmann, Dana Pe'er, Charles M. Rudin

Small cell lung cancer (SCLC) is an aggressive malignancy that includes subtypes defined by differential expression of ASCL1, NEUROD1, and POU2F3 (SCLC-A, -N, and -P, respectively). To define the heterogeneity of tumors and their associated microenvironments across subtypes, we sequenced 155,098 transcriptomes from 21 human biospecimens, including 54,523 SCLC transcriptomes. We observe greater tumor diversity in SCLC than lung adenocarcinoma, driven by canonical, intermediate, and admixed subtypes. We discover a PLCG2-high SCLC phenotype with stem-like, pro-metastatic features that recurs across subtypes and predicts worse overall survival. SCLC exhibits greater immune sequestration and less immune infiltration than lung adenocarcinoma, and SCLC-N shows less immune infiltrate and greater T cell dysfunction than SCLC-A. We identify a profibrotic, immunosuppressive monocyte/macrophage population in SCLC tumors that is particularly associated with the recurrent, PLCG2-high subpopulation.

Download bbrowser to analyze now

Species: human
Number of cells: 46140
Number of downloads: 7
Study size: 631MB
Uploaded at:

Immunology 
immuno-oncology 
Human Cell Atlas 
lung adenocarcinoma 
Cancer 
Small cell lung cancer 
Non-small cell lung cancer 

Signatures of plasticity, metastasis, and immunosuppression in an atlas of human small cell lung cancer (Combined T cells)

Joseph M. Chan, Álvaro Quintanal-Villalonga, Vianne Ran Gao, Yubin Xie, Viola Allaj, Ojasvi Chaudhary, Ignas Masilionis, Jacklynn Egger, Andrew Chow, Thomas Walle, Marissa Mattar, Dig V.K. Yarlagadda, James L. Wang, Fathema Uddin, Michael Offin, Metamia Ciampricotti, Besnik Qeriqi, Amber Bahr, Elisa de Stanchina, Umesh K. Bhanot, W. Victoria Lai, Matthew J. Bott, David R. Jones, Arvin Ruiz, Marina K. Baine, Yanyun Li, Natasha Rekhtman, John T. Poirier, Tal Nawy, Triparna Sen, Linas Mazutis, Travis J. Hollmann, Dana Pe'er, Charles M. Rudin

Small cell lung cancer (SCLC) is an aggressive malignancy that includes subtypes defined by differential expression of ASCL1, NEUROD1, and POU2F3 (SCLC-A, -N, and -P, respectively). To define the heterogeneity of tumors and their associated microenvironments across subtypes, we sequenced 155,098 transcriptomes from 21 human biospecimens, including 54,523 SCLC transcriptomes. We observe greater tumor diversity in SCLC than lung adenocarcinoma, driven by canonical, intermediate, and admixed subtypes. We discover a PLCG2-high SCLC phenotype with stem-like, pro-metastatic features that recurs across subtypes and predicts worse overall survival. SCLC exhibits greater immune sequestration and less immune infiltration than lung adenocarcinoma, and SCLC-N shows less immune infiltrate and greater T cell dysfunction than SCLC-A. We identify a profibrotic, immunosuppressive monocyte/macrophage population in SCLC tumors that is particularly associated with the recurrent, PLCG2-high subpopulation.

Download bbrowser to analyze now

Species: human
Number of cells: 14072
Number of downloads: 6
Study size: 352MB
Uploaded at:

Immunology 
immuno-oncology 
Human Cell Atlas 
lung adenocarcinoma 
Cancer 
Small cell lung cancer 
Non-small cell lung cancer 

Signatures of plasticity, metastasis, and immunosuppression in an atlas of human small cell lung cancer (Combined myeloid)

Joseph M. Chan, Álvaro Quintanal-Villalonga, Vianne Ran Gao, Yubin Xie, Viola Allaj, Ojasvi Chaudhary, Ignas Masilionis, Jacklynn Egger, Andrew Chow, Thomas Walle, Marissa Mattar, Dig V.K. Yarlagadda, James L. Wang, Fathema Uddin, Michael Offin, Metamia Ciampricotti, Besnik Qeriqi, Amber Bahr, Elisa de Stanchina, Umesh K. Bhanot, W. Victoria Lai, Matthew J. Bott, David R. Jones, Arvin Ruiz, Marina K. Baine, Yanyun Li, Natasha Rekhtman, John T. Poirier, Tal Nawy, Triparna Sen, Linas Mazutis, Travis J. Hollmann, Dana Pe'er, Charles M. Rudin

Small cell lung cancer (SCLC) is an aggressive malignancy that includes subtypes defined by differential expression of ASCL1, NEUROD1, and POU2F3 (SCLC-A, -N, and -P, respectively). To define the heterogeneity of tumors and their associated microenvironments across subtypes, we sequenced 155,098 transcriptomes from 21 human biospecimens, including 54,523 SCLC transcriptomes. We observe greater tumor diversity in SCLC than lung adenocarcinoma, driven by canonical, intermediate, and admixed subtypes. We discover a PLCG2-high SCLC phenotype with stem-like, pro-metastatic features that recurs across subtypes and predicts worse overall survival. SCLC exhibits greater immune sequestration and less immune infiltration than lung adenocarcinoma, and SCLC-N shows less immune infiltrate and greater T cell dysfunction than SCLC-A. We identify a profibrotic, immunosuppressive monocyte/macrophage population in SCLC tumors that is particularly associated with the recurrent, PLCG2-high subpopulation.

Download bbrowser to analyze now

Species: human
Number of cells: 8030
Number of downloads: 4
Study size: 191MB
Uploaded at:

Immunology 
immuno-oncology 
Human Cell Atlas 
lung adenocarcinoma 
Cancer 
Small cell lung cancer 
Non-small cell lung cancer 

Signatures of plasticity, metastasis, and immunosuppression in an atlas of human small cell lung cancer (Mesenchymal)

Joseph M. Chan, Álvaro Quintanal-Villalonga, Vianne Ran Gao, Yubin Xie, Viola Allaj, Ojasvi Chaudhary, Ignas Masilionis, Jacklynn Egger, Andrew Chow, Thomas Walle, Marissa Mattar, Dig V.K. Yarlagadda, James L. Wang, Fathema Uddin, Michael Offin, Metamia Ciampricotti, Besnik Qeriqi, Amber Bahr, Elisa de Stanchina, Umesh K. Bhanot, W. Victoria Lai, Matthew J. Bott, David R. Jones, Arvin Ruiz, Marina K. Baine, Yanyun Li, Natasha Rekhtman, John T. Poirier, Tal Nawy, Triparna Sen, Linas Mazutis, Travis J. Hollmann, Dana Pe'er, Charles M. Rudin

Small cell lung cancer (SCLC) is an aggressive malignancy that includes subtypes defined by differential expression of ASCL1, NEUROD1, and POU2F3 (SCLC-A, -N, and -P, respectively). To define the heterogeneity of tumors and their associated microenvironments across subtypes, we sequenced 155,098 transcriptomes from 21 human biospecimens, including 54,523 SCLC transcriptomes. We observe greater tumor diversity in SCLC than lung adenocarcinoma, driven by canonical, intermediate, and admixed subtypes. We discover a PLCG2-high SCLC phenotype with stem-like, pro-metastatic features that recurs across subtypes and predicts worse overall survival. SCLC exhibits greater immune sequestration and less immune infiltration than lung adenocarcinoma, and SCLC-N shows less immune infiltrate and greater T cell dysfunction than SCLC-A. We identify a profibrotic, immunosuppressive monocyte/macrophage population in SCLC tumors that is particularly associated with the recurrent, PLCG2-high subpopulation.

Download bbrowser to analyze now

Species: human
Number of cells: 9778
Number of downloads: 7
Study size: 273MB
Uploaded at:

Immunology 
immuno-oncology 
Human Cell Atlas 
lung adenocarcinoma 
Cancer 
Small cell lung cancer 
Non-small cell lung cancer 

Signatures of plasticity, metastasis, and immunosuppression in an atlas of human small cell lung cancer (NSCLC epithelial cells)

Joseph M. Chan, Álvaro Quintanal-Villalonga, Vianne Ran Gao, Yubin Xie, Viola Allaj, Ojasvi Chaudhary, Ignas Masilionis, Jacklynn Egger, Andrew Chow, Thomas Walle, Marissa Mattar, Dig V.K. Yarlagadda, James L. Wang, Fathema Uddin, Michael Offin, Metamia Ciampricotti, Besnik Qeriqi, Amber Bahr, Elisa de Stanchina, Umesh K. Bhanot, W. Victoria Lai, Matthew J. Bott, David R. Jones, Arvin Ruiz, Marina K. Baine, Yanyun Li, Natasha Rekhtman, John T. Poirier, Tal Nawy, Triparna Sen, Linas Mazutis, Travis J. Hollmann, Dana Pe'er, Charles M. Rudin

Small cell lung cancer (SCLC) is an aggressive malignancy that includes subtypes defined by differential expression of ASCL1, NEUROD1, and POU2F3 (SCLC-A, -N, and -P, respectively). To define the heterogeneity of tumors and their associated microenvironments across subtypes, we sequenced 155,098 transcriptomes from 21 human biospecimens, including 54,523 SCLC transcriptomes. We observe greater tumor diversity in SCLC than lung adenocarcinoma, driven by canonical, intermediate, and admixed subtypes. We discover a PLCG2-high SCLC phenotype with stem-like, pro-metastatic features that recurs across subtypes and predicts worse overall survival. SCLC exhibits greater immune sequestration and less immune infiltration than lung adenocarcinoma, and SCLC-N shows less immune infiltrate and greater T cell dysfunction than SCLC-A. We identify a profibrotic, immunosuppressive monocyte/macrophage population in SCLC tumors that is particularly associated with the recurrent, PLCG2-high subpopulation.

Download bbrowser to analyze now

Species: human
Number of cells: 2649
Number of downloads: 18
Study size: 53MB
Uploaded at:

Intestine 
Intestinal development 
STAR-FINDer 
Spatio-temporal analysis 

Spatiotemporal analysis of human intestinal development at single-cell resolution (Slide A1)

David Fawkner-Corbett, Agne Antanaviciute, Kaushal Parikh, Marta Jagielowicz, Ana Sousa Gerós, Tarun Gupta, Neil Ashley, Doran Khamis, Darren Fowler, Edward Morrissey, Chris Cunningham, Paul R.V. Johnson, Hashem Koohy, Alison Simmons

Development of the human intestine is not well understood. Here, we link single-cell RNA sequencing and spatial transcriptomics to characterize intestinal morphogenesis through time. We identify 101 cell states including epithelial and mesenchymal progenitor populations and programs linked to key morphogenetic milestones. We describe principles of crypt-villus axis formation; neural, vascular, mesenchymal morphogenesis, and immune population of the developing gut. We identify the differentiation hierarchies of developing fibroblast and myofibroblast subtypes and describe diverse functions for these including as vascular niche cells. We pinpoint the origins of Peyer’s patches and gut-associated lymphoid tissue (GALT) and describe location-specific immune programs. We use our resource to present an unbiased analysis of morphogen gradients that direct sequential waves of cellular differentiation and define cells and locations linked to rare developmental intestinal disorders. We compile a publicly available online resource, spatio-temporal analysis resource of fetal intestinal development (STAR-FINDer), to facilitate further work.

Download bbrowser to analyze now

Species: human
Number of cells: 2316
Number of downloads: 6
Study size: 66MB
Uploaded at:

Intestine 
Intestinal development 
STAR-FINDer 
Spatio-temporal analysis 

Spatiotemporal analysis of human intestinal development at single-cell resolution (Slide A2)

David Fawkner-Corbett, Agne Antanaviciute, Kaushal Parikh, Marta Jagielowicz, Ana Sousa Gerós, Tarun Gupta, Neil Ashley, Doran Khamis, Darren Fowler, Edward Morrissey, Chris Cunningham, Paul R.V. Johnson, Hashem Koohy, Alison Simmons

Development of the human intestine is not well understood. Here, we link single-cell RNA sequencing and spatial transcriptomics to characterize intestinal morphogenesis through time. We identify 101 cell states including epithelial and mesenchymal progenitor populations and programs linked to key morphogenetic milestones. We describe principles of crypt-villus axis formation; neural, vascular, mesenchymal morphogenesis, and immune population of the developing gut. We identify the differentiation hierarchies of developing fibroblast and myofibroblast subtypes and describe diverse functions for these including as vascular niche cells. We pinpoint the origins of Peyer’s patches and gut-associated lymphoid tissue (GALT) and describe location-specific immune programs. We use our resource to present an unbiased analysis of morphogen gradients that direct sequential waves of cellular differentiation and define cells and locations linked to rare developmental intestinal disorders. We compile a publicly available online resource, spatio-temporal analysis resource of fetal intestinal development (STAR-FINDer), to facilitate further work.

Download bbrowser to analyze now

Species: human
Number of cells: 1080
Number of downloads: 5
Study size: 34MB
Uploaded at:

Intestine 
Intestinal development 
STAR-FINDer 
Spatio-temporal analysis 

Spatiotemporal analysis of human intestinal development at single-cell resolution (Slide A3)

David Fawkner-Corbett, Agne Antanaviciute, Kaushal Parikh, Marta Jagielowicz, Ana Sousa Gerós, Tarun Gupta, Neil Ashley, Doran Khamis, Darren Fowler, Edward Morrissey, Chris Cunningham, Paul R.V. Johnson, Hashem Koohy, Alison Simmons

Development of the human intestine is not well understood. Here, we link single-cell RNA sequencing and spatial transcriptomics to characterize intestinal morphogenesis through time. We identify 101 cell states including epithelial and mesenchymal progenitor populations and programs linked to key morphogenetic milestones. We describe principles of crypt-villus axis formation; neural, vascular, mesenchymal morphogenesis, and immune population of the developing gut. We identify the differentiation hierarchies of developing fibroblast and myofibroblast subtypes and describe diverse functions for these including as vascular niche cells. We pinpoint the origins of Peyer’s patches and gut-associated lymphoid tissue (GALT) and describe location-specific immune programs. We use our resource to present an unbiased analysis of morphogen gradients that direct sequential waves of cellular differentiation and define cells and locations linked to rare developmental intestinal disorders. We compile a publicly available online resource, spatio-temporal analysis resource of fetal intestinal development (STAR-FINDer), to facilitate further work.

Download bbrowser to analyze now

Species: human
Number of cells: 1242
Number of downloads: 3
Study size: 43MB
Uploaded at:

Intestine 
Intestinal development 
STAR-FINDer 
Spatio-temporal analysis 

Spatiotemporal analysis of human intestinal development at single-cell resolution (Slide A4)

David Fawkner-Corbett, Agne Antanaviciute, Kaushal Parikh, Marta Jagielowicz, Ana Sousa Gerós, Tarun Gupta, Neil Ashley, Doran Khamis, Darren Fowler, Edward Morrissey, Chris Cunningham, Paul R.V. Johnson, Hashem Koohy, Alison Simmons

Development of the human intestine is not well understood. Here, we link single-cell RNA sequencing and spatial transcriptomics to characterize intestinal morphogenesis through time. We identify 101 cell states including epithelial and mesenchymal progenitor populations and programs linked to key morphogenetic milestones. We describe principles of crypt-villus axis formation; neural, vascular, mesenchymal morphogenesis, and immune population of the developing gut. We identify the differentiation hierarchies of developing fibroblast and myofibroblast subtypes and describe diverse functions for these including as vascular niche cells. We pinpoint the origins of Peyer’s patches and gut-associated lymphoid tissue (GALT) and describe location-specific immune programs. We use our resource to present an unbiased analysis of morphogen gradients that direct sequential waves of cellular differentiation and define cells and locations linked to rare developmental intestinal disorders. We compile a publicly available online resource, spatio-temporal analysis resource of fetal intestinal development (STAR-FINDer), to facilitate further work.

Download bbrowser to analyze now

About 606 datasets