Single-cell and spatial transcriptomics reveal aberrant lymphoid developmental programs driving granuloma formation

(SNP Array) Single-Cell Multi-Omics Identifies Chronic Inflammation as a Driver of TP53 mutant Leukaemic Evolution

Rodriguez-Meira, Alba

June 2023

Single nucleotide polymorphism (SNP) array data files related our publication titled "Single-Cell Mu...

Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data

Geras, Agnieszka
Darvish Shafighi, Shadi
Domżał, Kacper
Filipiuk, Igor
Rączkowski, Łukasz
Szymczak, Paulina
Toosi, Hosein
Kaczmarek, Leszek
Koperski, Łukasz
Lagergren, Jens
Nowis, Dominika
Szczurek, Ewa

February 2023

Code necessary to reproduce the analyses presented in the manuscript: Celloscope: a probabilistic mo...

Supporting code for "Molecular phenotyping reveals the identity of Barrett's esophagus and its malignant transition"

Nowicki-Osuch, Karol

May 2021

Supporting code for "Molecular phenotyping reveals the identity of Barrett's esophagus and its malig...

Single-cell and spatial transcriptomics reveal aberrant lymphoid developmental programs driving granuloma formation

Krausgruber, Thomas
Redl, Anna
Barreca, Daniele
Doberer, Konstantin
Romanovskaia, Daria
Dobnikar, Lina
Guarini, Maria
Unterluggauer, Luisa
Kleissl, Lisa
Atzmüller, Denise
Mayerhofer, Carolina
Kopf, Aglaja
Saluzzo, Simona
Lim, Clarice X.
Rexie, Praveen
Weichhart, Thomas
Bock, Christoph
Stary, Georg

January 2023

This is the codebase for data analysis, underlying the publication "Single-cell and spatial transcri...

(Preprocessing) Single-Cell Multi-Omics Identifies Chronic Inflammation as a Driver of TP53 mutant Leukaemic Evolution

Rodriguez-Meira, Alba
Wen, Sean

June 2023

Files and scripts for preprocessing of dataset related to our publication titled "Single-Cell Multi-...

Identifying cell type-specific proliferation signatures in spatial transcriptomics data and inferring interactions driving tumour growth

Wærn, Felix

January 2023

Cancer is a dangerous disease caused by mutations in the host's genome that makes the cells prolifer...

Single-cell heterogeneity of EGFR and CKD4 co-amplification is linked to immune infiltration in glioblastoma

Simona

February 2023

This upload contains RDS objects of preprocessed publicly available scRNAseq data, required to run s...

Single-Cell Multi-Omics Identifies Chronic Inflammation as a Driver of TP53 mutant Leukaemic Evolution

Rodriguez-Meira, Alba

June 2023

Files to reproduce all figures related the our publication titled "Single-Cell Multi-Omics Identifie...

Single-cell and spatial transcriptomics enables probabilistic inference of cell type topography

Alma Andersson

July 2020

Code associated with the publication "Single-cell and spatial transcriptomics enables probabilistic ...

Single-cell transcriptomics identifies synergistic role of leukemic and non-leukemic immune repertoires in CD8+ T-cell Large Granular Lymphocytic Leukemia

Huuhtanen Jani
Bhattacharya Dipabarna
Mustjoki Satu

December 2021

Data to reproduce findings in the manuscript "Single-cell transcriptomics identifies synergistic rol...

Spatial and temporal localization of immune transcripts defines hallmarks and diversity in the tuberculosis granuloma

Berit Carow (6193646)
Thomas Hauling (5804096)
Xiaoyan Qian (1572298)
Igor Kramnik (183572)
Mats Nilsson (7964)
Martin Rottenberg (6288964)

March 2019

This repository contains raw data and all scripts for the in situ sequencing processing pipeline (Ma...

Spatial transcriptomics of B and T cell receptors uncovers lymphocyte clonal dynamics.

Camilla Engblom
Kim Thrane
Qirong Lin
Alma Andersson
Hosein Toosi
Xinsong Chen
Embla Steiner
Chang Lu
Giulia Mantovani
Michael Hagemann-Jensen
Sami Saarenpää
Mattias Jangard
Julio Saez-Rodriguez
Jakob Michaëlsson
Johan Hartman
Jens Lagergren
Jeff Mold
Joakim Lundeberg
Jonas Frisén

November 2022

This dataset contains a single zipped folder containing: data scripts needed to reprod...

Expression, processing and transcriptional regulation of granulysin in short-term activated human lymphocytes-5

Sonja Latinovic-Golic (63498)
Michael Walch (6848)
Hanna Sundstrom (63499)
Claudia Dumrese (6844)
Peter Groscurth (6849)
Urs Ziegler (6850)

December 2011

Copyright information:Taken from "Expression, processing and transcriptional regula...

Spatial transcriptomics of T and B cell receptors uncovers lymphocyte clonal dynamics in human tissue.

Camilla Engblom
Kim Thrane
Qirong Lin
Alma Andersson
Hosein Toosi
Xinsong Chen
Embla Steiner
Giulia Mantovani
Michael Hagemann-Jensen
Sami Saarenpää
Mattias Jangard
Jakob Michaëlsson
Johan Hartman
Jens Lagergren
Jeff Mold
Joakim Lundeberg
Jonas Frisén

November 2022

This dataset contains a single zipped folder containing: data scripts needed to reprod...

Integration of Transcriptomic and Proteomic Data during Nucleus Lobulation of Granulocytes

Ranjbar, Niloufar

May 2021

Nucleus is the origin of most phenotypic activities in a cell. Depending on the cell type, the nucle...

(SNP Array) Single-Cell Multi-Omics Identifies Chronic Inflammation as a Driver of TP53 mutant Leukaemic Evolution

Rodriguez-Meira, Alba

June 2023

Single nucleotide polymorphism (SNP) array data files related our publication titled "Single-Cell Mu...

Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data

Geras, Agnieszka
Darvish Shafighi, Shadi
Domżał, Kacper
Filipiuk, Igor
Rączkowski, Łukasz
Szymczak, Paulina
Toosi, Hosein
Kaczmarek, Leszek
Koperski, Łukasz
Lagergren, Jens
Nowis, Dominika
Szczurek, Ewa

February 2023

Code necessary to reproduce the analyses presented in the manuscript: Celloscope: a probabilistic mo...

Supporting code for "Molecular phenotyping reveals the identity of Barrett's esophagus and its malignant transition"

Nowicki-Osuch, Karol

May 2021

Supporting code for "Molecular phenotyping reveals the identity of Barrett's esophagus and its malig...

Single-cell and spatial transcriptomics reveal aberrant lymphoid developmental programs driving granuloma formation

Krausgruber, Thomas
Redl, Anna
Barreca, Daniele
Doberer, Konstantin
Romanovskaia, Daria
Dobnikar, Lina
Guarini, Maria
Unterluggauer, Luisa
Kleissl, Lisa
Atzmüller, Denise
Mayerhofer, Carolina
Kopf, Aglaja
Saluzzo, Simona
Lim, Clarice X.
Rexie, Praveen
Weichhart, Thomas
Bock, Christoph
Stary, Georg

January 2023

This is the codebase for data analysis, underlying the publication "Single-cell and spatial transcri...

(Preprocessing) Single-Cell Multi-Omics Identifies Chronic Inflammation as a Driver of TP53 mutant Leukaemic Evolution

Rodriguez-Meira, Alba
Wen, Sean

June 2023

Files and scripts for preprocessing of dataset related to our publication titled "Single-Cell Multi-...

Identifying cell type-specific proliferation signatures in spatial transcriptomics data and inferring interactions driving tumour growth

Wærn, Felix

January 2023

Cancer is a dangerous disease caused by mutations in the host's genome that makes the cells prolifer...

Single-cell heterogeneity of EGFR and CKD4 co-amplification is linked to immune infiltration in glioblastoma

Simona

February 2023

This upload contains RDS objects of preprocessed publicly available scRNAseq data, required to run s...

Single-Cell Multi-Omics Identifies Chronic Inflammation as a Driver of TP53 mutant Leukaemic Evolution

Rodriguez-Meira, Alba

June 2023

Files to reproduce all figures related the our publication titled "Single-Cell Multi-Omics Identifie...

Single-cell and spatial transcriptomics enables probabilistic inference of cell type topography

Alma Andersson

July 2020

Code associated with the publication "Single-cell and spatial transcriptomics enables probabilistic ...

Single-cell transcriptomics identifies synergistic role of leukemic and non-leukemic immune repertoires in CD8+ T-cell Large Granular Lymphocytic Leukemia

Huuhtanen Jani
Bhattacharya Dipabarna
Mustjoki Satu

December 2021

Data to reproduce findings in the manuscript "Single-cell transcriptomics identifies synergistic rol...

Spatial and temporal localization of immune transcripts defines hallmarks and diversity in the tuberculosis granuloma

Berit Carow (6193646)
Thomas Hauling (5804096)
Xiaoyan Qian (1572298)
Igor Kramnik (183572)
Mats Nilsson (7964)
Martin Rottenberg (6288964)

March 2019

This repository contains raw data and all scripts for the in situ sequencing processing pipeline (Ma...

Spatial transcriptomics of B and T cell receptors uncovers lymphocyte clonal dynamics.

Camilla Engblom
Kim Thrane
Qirong Lin
Alma Andersson
Hosein Toosi
Xinsong Chen
Embla Steiner
Chang Lu
Giulia Mantovani
Michael Hagemann-Jensen
Sami Saarenpää
Mattias Jangard
Julio Saez-Rodriguez
Jakob Michaëlsson
Johan Hartman
Jens Lagergren
Jeff Mold
Joakim Lundeberg
Jonas Frisén

November 2022

This dataset contains a single zipped folder containing: data scripts needed to reprod...

Expression, processing and transcriptional regulation of granulysin in short-term activated human lymphocytes-5

Sonja Latinovic-Golic (63498)
Michael Walch (6848)
Hanna Sundstrom (63499)
Claudia Dumrese (6844)
Peter Groscurth (6849)
Urs Ziegler (6850)

December 2011

Copyright information:Taken from "Expression, processing and transcriptional regula...

Spatial transcriptomics of T and B cell receptors uncovers lymphocyte clonal dynamics in human tissue.

Camilla Engblom
Kim Thrane
Qirong Lin
Alma Andersson
Hosein Toosi
Xinsong Chen
Embla Steiner
Giulia Mantovani
Michael Hagemann-Jensen
Sami Saarenpää
Mattias Jangard
Jakob Michaëlsson
Johan Hartman
Jens Lagergren
Jeff Mold
Joakim Lundeberg
Jonas Frisén

November 2022

This dataset contains a single zipped folder containing: data scripts needed to reprod...

Integration of Transcriptomic and Proteomic Data during Nucleus Lobulation of Granulocytes

Ranjbar, Niloufar

May 2021

Nucleus is the origin of most phenotypic activities in a cell. Depending on the cell type, the nucle...

(SNP Array) Single-Cell Multi-Omics Identifies Chronic Inflammation as a Driver of TP53 mutant Leukaemic Evolution

Rodriguez-Meira, Alba

June 2023

Single nucleotide polymorphism (SNP) array data files related our publication titled "Single-Cell Mu...

Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data

Geras, Agnieszka
Darvish Shafighi, Shadi
Domżał, Kacper
Filipiuk, Igor
Rączkowski, Łukasz
Szymczak, Paulina
Toosi, Hosein
Kaczmarek, Leszek
Koperski, Łukasz
Lagergren, Jens
Nowis, Dominika
Szczurek, Ewa

February 2023

Code necessary to reproduce the analyses presented in the manuscript: Celloscope: a probabilistic mo...

Supporting code for "Molecular phenotyping reveals the identity of Barrett's esophagus and its malignant transition"

Nowicki-Osuch, Karol

May 2021

Supporting code for "Molecular phenotyping reveals the identity of Barrett's esophagus and its malig...

Single-cell and spatial transcriptomics reveal aberrant lymphoid developmental programs driving granuloma formation

Abstract

Extracted data

Single-cell and spatial transcriptomics reveal aberrant lymphoid developmental programs driving granuloma formation

Abstract

Extracted data

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