Reference quantitative transcriptome dataset for adult Caenorhabditis elegans
Caenorhabditis elegans is a nematode widely used in biology and genomics as a model organism. We provide an integrated, quantitative reference map for the transcriptome of whole, wild type Bristol N2 strain C. elegans worms. The map has been obtained by meta-analysis of 110 gene expression profiles...
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doaj-c5bb96cb969549409e1fccc24cc484672020-11-25T01:50:36ZengElsevierData in Brief2352-34092019-08-0125Reference quantitative transcriptome dataset for adult Caenorhabditis elegansAllison Piovesan0Francesca Antonaros1Pierluigi Strippoli2Lorenza Vitale3Maria Chiara Pelleri4Maria Caracausi5Department of Experimental, Diagnostic and Specialty Medicine, (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126 Bologna, BO, ItalyDepartment of Experimental, Diagnostic and Specialty Medicine, (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126 Bologna, BO, ItalyDepartment of Experimental, Diagnostic and Specialty Medicine, (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126 Bologna, BO, ItalyDepartment of Experimental, Diagnostic and Specialty Medicine, (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126 Bologna, BO, ItalyCorresponding author.; Department of Experimental, Diagnostic and Specialty Medicine, (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126 Bologna, BO, ItalyDepartment of Experimental, Diagnostic and Specialty Medicine, (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126 Bologna, BO, ItalyCaenorhabditis elegans is a nematode widely used in biology and genomics as a model organism. We provide an integrated, quantitative reference map for the transcriptome of whole, wild type Bristol N2 strain C. elegans worms. The map has been obtained by meta-analysis of 110 gene expression profiles available in Gene Expression Omnibus (GEO) repository and integrated using the computational biology tool Transcriptome Mapper (TRAM). Following probe assignment to the relative locus and intra- and inter-sample normalization (in particular using the scaled quantile method), a mean, consensus reference value is provided for 45,932 transcripts, along with standard deviation. Expression values are all mapped in the context of genomic coordinates. The map provides easy access to relationships among expression values of different genes in this standard condition, highlights genomic segments with relatively high over-/under-expression and may serve as a reference to test for gene expression variation for both individual genes and the whole transcriptome in specific biological conditions (e.g. mutated strains or differently grown worms). Keywords: C. elegans, Transcriptome map, Gene expression, Adult worms, Meta-analysishttp://www.sciencedirect.com/science/article/pii/S2352340919305062 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Allison Piovesan Francesca Antonaros Pierluigi Strippoli Lorenza Vitale Maria Chiara Pelleri Maria Caracausi |
spellingShingle |
Allison Piovesan Francesca Antonaros Pierluigi Strippoli Lorenza Vitale Maria Chiara Pelleri Maria Caracausi Reference quantitative transcriptome dataset for adult Caenorhabditis elegans Data in Brief |
author_facet |
Allison Piovesan Francesca Antonaros Pierluigi Strippoli Lorenza Vitale Maria Chiara Pelleri Maria Caracausi |
author_sort |
Allison Piovesan |
title |
Reference quantitative transcriptome dataset for adult Caenorhabditis elegans |
title_short |
Reference quantitative transcriptome dataset for adult Caenorhabditis elegans |
title_full |
Reference quantitative transcriptome dataset for adult Caenorhabditis elegans |
title_fullStr |
Reference quantitative transcriptome dataset for adult Caenorhabditis elegans |
title_full_unstemmed |
Reference quantitative transcriptome dataset for adult Caenorhabditis elegans |
title_sort |
reference quantitative transcriptome dataset for adult caenorhabditis elegans |
publisher |
Elsevier |
series |
Data in Brief |
issn |
2352-3409 |
publishDate |
2019-08-01 |
description |
Caenorhabditis elegans is a nematode widely used in biology and genomics as a model organism. We provide an integrated, quantitative reference map for the transcriptome of whole, wild type Bristol N2 strain C. elegans worms. The map has been obtained by meta-analysis of 110 gene expression profiles available in Gene Expression Omnibus (GEO) repository and integrated using the computational biology tool Transcriptome Mapper (TRAM). Following probe assignment to the relative locus and intra- and inter-sample normalization (in particular using the scaled quantile method), a mean, consensus reference value is provided for 45,932 transcripts, along with standard deviation. Expression values are all mapped in the context of genomic coordinates. The map provides easy access to relationships among expression values of different genes in this standard condition, highlights genomic segments with relatively high over-/under-expression and may serve as a reference to test for gene expression variation for both individual genes and the whole transcriptome in specific biological conditions (e.g. mutated strains or differently grown worms). Keywords: C. elegans, Transcriptome map, Gene expression, Adult worms, Meta-analysis |
url |
http://www.sciencedirect.com/science/article/pii/S2352340919305062 |
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