scholarly journals The spatial landscape of gene expression isoforms in tissue sections

2020 ◽  
Author(s):  
Kevin Lebrigand ◽  
Joseph Bergenstråhle ◽  
Kim Thrane ◽  
Annelie Mollbrink ◽  
Pascal Barbry ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Data ◽  
Biological Systems ◽  
Full Length ◽  
Expression Data ◽  
Sequence Heterogeneity ◽  
Tissue Sections ◽  
Splicing Variants ◽  
Full Length Sequence

ABSTRACTIn situ capturing technologies add tissue context to gene expression data, with the potential of providing a greater understanding of complex biological systems. However, splicing variants and full-length sequence heterogeneity cannot be characterized with current methods. Here, we introduce Spatial Isoform Transcriptomics (SiT), an explorative method for characterizing spatial isoform and sequence heterogeneity in tissue sections, and show how it can be used to profile isoform expression and sequence heterogeneity in a tissue context

scholarly journals A regression system for estimation of errors introduced by confocal imaging into gene expression data in situ

2011 ◽  
Vol 12 (1) ◽  
Author(s):  
Ekaterina Myasnikova ◽  
Svetlana Surkova ◽  
Grigory Stein ◽  
Andrei Pisarev ◽  
Maria Samsonova
Keyword(s):  
Gene Expression ◽  
Gene Expression Data ◽  
Confocal Imaging ◽  
Expression Data

Mooshka: a system for the management of multidimensional gene expression data in situ

2003 ◽  
Vol 28 (4) ◽  
pp. 269-285 ◽  
Author(s):  
Andrei Pisarev ◽  
Ekaterina Poustelnikova ◽  
Maria Samsonova ◽  
Peter Baumann
Keyword(s):  
Gene Expression ◽  
Gene Expression Data ◽  
Expression Data

A database for management of gene expression data in situ

2004 ◽  
Vol 20 (14) ◽  
pp. 2212-2221 ◽  
Author(s):  
E. Poustelnikova ◽  
A. Pisarev ◽  
M. Blagov ◽  
M. Samsonova ◽  
J. Reinitz
Keyword(s):  
Gene Expression ◽  
Gene Expression Data ◽  
Expression Data

Erratum to “Mooshka: a system for the management of multidimensional gene expression data in situ”

2004 ◽  
Vol 29 (1) ◽  
pp. 93
Author(s):  
Andrei Pisarev ◽  
Ekaterina Poustelnikova ◽  
Maria Samsonova ◽  
Peter Baumann
Keyword(s):  
Gene Expression ◽  
Gene Expression Data ◽  
Expression Data

scholarly journals A Regression System for Estimation of Errors Introduced by Confocal Imaging into Gene Expression Data In Situ

2014 ◽  
pp. 77-103
Author(s):  
Ekaterina Myasnikova ◽  
Svetlana Surkova ◽  
Grigory Stein ◽  
Andrei Pisarev ◽  
Maria Samsonova
Keyword(s):  
Gene Expression ◽  
Gene Expression Data ◽  
Confocal Imaging ◽  
Expression Data

scholarly journals Clustered brachiopod Hox genes are not expressed collinearly and are associated with lophotrochozoan novelties

2016 ◽  
Author(s):  
Sabrina M. Schiemann ◽  
José M. Martín-Durán ◽  
Aina Børve ◽  
Bruno C. Vellutini ◽  
Yale J. Passamaneck ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Data ◽  
Molecular Basis ◽  
Hox Genes ◽  
Expression Data ◽  
Specific Expression ◽  
Spatial Expression ◽  
Morphological Novelties ◽  
Hox Clusters

AbstractTemporal collinearity is often regarded as the force preserving Hox clusters in vertebrate genomes. Studies that combine genomic and gene expression data in invertebrates would allow generalizing this observation across all animals, but are scarce, particularly within Lophotrochozoa (e.g., snails and segmented worms). Here, we use two brachiopod species –Terebratalia transversa, Novocrania anomala– to characterize the complement, cluster and expression of their Hox genes. T. transversa has an ordered, split cluster with ten genes (lab, pb, Hox3, dfd, scr, lox5, antp, lox4, post2, post1), while N. anomala has nine (missing post1). Our in situ hybridization, qPCR and stage specific transcriptomic analyses show that brachiopod Hox genes are neither strictly temporally nor spatially collinear; only pb (in T. transversa), Hox3 and dfd (in both brachiopods) show staggered mesodermal expression. The spatial expression of the Hox genes in both brachiopod species correlates with their morphology and demonstrates cooption of Hox genes in the chaetae and shell fields, two major lophotrochozoan morphological novelties. The shared and specific expression of a subset of Hox genes, Arx and Zic orthologs in chaetae and shell-fields between brachiopods, mollusks, and annelids supports the deep conservation of the molecular basis forming these lophotrochozoan hallmarks. Our findings challenge that collinearity alone preserves lophotrochozoan Hox clusters, indicating that additional genomic traits need to be considered in understanding Hox evolution.

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