FAIRsharing.k6a8e5; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:22.439109

newt-omics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:22.439109

Other names: newt-omics

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A comprehensive repository for omics data from the red spotted newt Notophthalmus viridescens from high throughput experiments. Newt-Omics aims to provide a comprehensive platform of expressed genes during tissue regeneration, including extensive annotations, expression data and experimentally verified peptide sequences with yet no homology to other publically available gene sequences. The goal is to obtain a detailed understanding of the molecular processes underlying tissue regeneration in the newt,that may lead to the development of approaches, efficiently stimulating regenerative pathways in mammalians.

Webpage:

http://newt-omics.mpi-bn.mpg.de

Publications:

Publications
More detailed information about this field from each metasource.

A de novo assembly of the newt transcriptome combined with proteomic validation identifies new protein families expressed during tissue regeneration
PMID: 23425577
metasource: Fairsharing.org
version: FAIRsharing.org: Newt-omics; Newt-omics; DOI: https://doi.org/10.25504/FAIRsharing.k6a8e5; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

Advanced identification of proteins in uncharacterized proteomes by pulsed in vivo stable isotope labeling-based mass spectrometry
PMID: 20139370
metasource: Fairsharing.org
version: FAIRsharing.org: Newt-omics; Newt-omics; DOI: https://doi.org/10.25504/FAIRsharing.k6a8e5; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

Analysis of newly established EST databases reveals similarities between heart regeneration in newt and fish
PMID: 20047682
metasource: Fairsharing.org
version: FAIRsharing.org: Newt-omics; Newt-omics; DOI: https://doi.org/10.25504/FAIRsharing.k6a8e5; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

Newt-omics: a comprehensive repository for omics data from the newt Notophthalmus viridescens
PMID: 22039101
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:22.439109

http://dx.doi.org/10.1093/nar/GKR873
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

A de novo assembly of the newt transcriptome combined with proteomic validation identifies new protein families expressed during tissue regeneration PubMed citations: 46.

46 articles citing: A de novo assembly of the newt transcriptome combined with proteomic validation identifies new protein families expressed during tissue regeneration

From Autonomy to Integration, From Integration to Dynamically Balanced Integrated Co-existence: Non-aging as the Third Stage of Development. PMID:35822034
Newt regeneration genes regulate Wingless signaling to restore patterning in Drosophila eye. PMID:34746690
Relationship between the Phenylpropanoid Pathway and Dwarfism of Paspalum seashore Based on RNA-Seq and iTRAQ. PMID:34502485
Single-cell RNA-seq reveals novel mitochondria-related musculoskeletal cell populations during adult axolotl limb regeneration process. PMID:33116295
Proteomics of Galápagos Marine Iguanas Links Function of Femoral Gland Proteins to the Immune System. PMID:32581039
Towards comparative analyses of salamander limb regeneration. PMID:31584252
Comparative transcriptomic analysis and structure prediction of novel Newt proteins. PMID:31419228
Model systems for regeneration: salamanders. PMID:31332037
Insights into regeneration tool box: An animal model approach. PMID:30986388
The First Transcriptome Assembly of Yenyuan Stream Salamander (Batrachuperus yenyuanensis) Provides Novel Insights into Its Molecular Evolution. PMID:30934682
Using transcriptomics to enable a plethodontid salamander (Bolitoglossa ramosi) for limb regeneration research. PMID:30253734
Lens regeneration: a historical perspective. PMID:29877565
Novel erythrocyte clumps revealed by an orphan gene Newtic1 in circulating blood and regenerating limbs of the adult newt. PMID:29748592
Evolution, comparative biology and ontogeny of vertebrate heart regeneration. PMID:29302337
Mechanisms of urodele limb regeneration. PMID:29299322
Reading and editing the Pleurodeles waltl genome reveals novel features of tetrapod regeneration. PMID:29273779
Molecular Convergent Evolution of the MYBPC2 Gene Among Three High-Elevation Amphibian Species. PMID:28220195
A Tissue-Mapped Axolotl De Novo Transcriptome Enables Identification of Limb Regeneration Factors. PMID:28099853
Tetrapod limb and sarcopterygian fin regeneration share a core genetic programme. PMID:27804976
A linkage map for the Newt Notophthalmus viridescens: Insights in vertebrate genome and chromosome evolution. PMID:27265323
RNA-Seq and iTRAQ Reveal the Dwarfing Mechanism of Dwarf Polish Wheat (Triticum polonicum L.). PMID:27194943
LimiTT: link miRNAs to targets. PMID:27170328
A dynamic architecture of life. PMID:26949518
Data set for transcriptome analysis of the Chinese giant salamander (Andrias davidianus ). PMID:26759822
Improvement of genome assembly completeness and identification of novel full-length protein-coding genes by RNA-seq in the giant panda genome. PMID:26658305
Transcriptomes reveal the genetic mechanisms underlying ionic regulatory adaptations to salt in the crab-eating frog. PMID:26619819
Genetic adaptations of the plateau zokor in high-elevation burrows. PMID:26602147
AlignWise: a tool for identifying protein-coding sequence and correcting frame-shifts. PMID:26553107
A robust transcriptional program in newts undergoing multiple events of lens regeneration throughout their lifespan. PMID:26523389
De novo assembly of the Japanese lawngrass (Zoysia japonica Steud.) root transcriptome and identification of candidate unigenes related to early responses under salt stress. PMID:26347751
Identification of the orphan gene Prod 1 in basal and other salamander families. PMID:25874078
A Comprehensive Transcriptomic and Proteomic Analysis of Hydra Head Regeneration. PMID:25841488
Social parasitism and the molecular basis of phenotypic evolution. PMID:25741361
Molecular signatures that correlate with induction of lens regeneration in newts: lessons from proteomic analysis. PMID:25496664
Integrative structural annotation of de novo RNA-Seq provides an accurate reference gene set of the enormous genome of the onion (Allium cepa L.). PMID:25362073
Transcriptome analysis elucidates key developmental components of bryozoan lophophore development. PMID:25300304
A transcriptome for the study of early processes of retinal regeneration in the adult newt, Cynops pyrrhogaster. PMID:25290450
Early evolution of limb regeneration in tetrapods: evidence from a 300-million-year-old amphibian. PMID:25253458
Transcriptomic analysis of tail regeneration in the lizard Anolis carolinensis reveals activation of conserved vertebrate developmental and repair mechanisms. PMID:25140675
On the optimal trimming of high-throughput mRNA sequence data. PMID:24567737
Cardiac regeneration in model organisms. PMID:24496965
Functional similarity and molecular divergence of a novel reproductive transcriptome in two male-pregnant Syngnathus pipefish species. PMID:24324861
The planarian regeneration transcriptome reveals a shared but temporally shifted regulatory program between opposing head and tail scenarios. PMID:24238224
Transcriptome profile of the green odorous frog (Odorrana margaretae). PMID:24073255
Transcriptome analysis of newt lens regeneration reveals distinct gradients in gene expression patterns. PMID:23613853
What is it about 'eye of newt'? PMID:23425551
Advanced identification of proteins in uncharacterized proteomes by pulsed in vivo stable isotope labeling-based mass spectrometry PubMed citations: 14.

14 articles citing: Advanced identification of proteins in uncharacterized proteomes by pulsed in vivo stable isotope labeling-based mass spectrometry

UNSUPERVISED DOMAIN ALIGNMENT BASED OPEN SET STRUCTURAL RECOGNITION OF MACROMOLECULES CAPTURED BY CRYO-ELECTRON TOMOGRAPHY. PMID:35350462
SILAC-based quantitative MS approach for real-time recording protein-mediated cell-cell interactions. PMID:29855483
Exploring ribosome composition and newly synthesized proteins through proteomics and potential biomedical applications. PMID:28532181
Molecular signatures that correlate with induction of lens regeneration in newts: lessons from proteomic analysis. PMID:25496664
Comparing SILAC- and stable isotope dimethyl-labeling approaches for quantitative proteomics. PMID:25077673
Deep proteomics of the Xenopus laevis egg using an mRNA-derived reference database. PMID:24954049
Integrative "omics"-approach discovers dynamic and regulatory features of bacterial stress responses. PMID:23818867
Automated, reproducible, titania-based phosphopeptide enrichment strategy for label-free quantitative phosphoproteomics. PMID:23542237
A de novo assembly of the newt transcriptome combined with proteomic validation identifies new protein families expressed during tissue regeneration. PMID:23425577
Stable isotope labeling in zebrafish allows in vivo monitoring of cardiac morphogenesis. PMID:23412571
Stable isotope labeling with amino acids in Drosophila for quantifying proteins and modifications. PMID:22830426
Newt-omics: a comprehensive repository for omics data from the newt Notophthalmus viridescens. PMID:22039101
Quantitative label-free phosphoproteomics strategy for multifaceted experimental designs. PMID:21491946
The SILAC fly allows for accurate protein quantification in vivo. PMID:20525996
Analysis of newly established EST databases reveals similarities between heart regeneration in newt and fish PubMed citations: 7.

7 articles citing: Analysis of newly established EST databases reveals similarities between heart regeneration in newt and fish

A Systematic Exposition of Methods used for Quantification of Heart Regeneration after Apex Resection in Zebrafish. PMID:32111059
A conserved HH-Gli1-Mycn network regulates heart regeneration from newt to human. PMID:30315164
Comparative RNA-seq analysis in the unsequenced axolotl: the oncogene burst highlights early gene expression in the blastema. PMID:23505351
A de novo assembly of the newt transcriptome combined with proteomic validation identifies new protein families expressed during tissue regeneration. PMID:23425577
Newt-omics: a comprehensive repository for omics data from the newt Notophthalmus viridescens. PMID:22039101
Deep sequencing-based transcriptome profiling analysis of bacteria-challenged Lateolabrax japonicus reveals insight into the immune-relevant genes in marine fish. PMID:20707909
Advanced identification of proteins in uncharacterized proteomes by pulsed in vivo stable isotope labeling-based mass spectrometry. PMID:20139370
Newt-omics: a comprehensive repository for omics data from the newt Notophthalmus viridescens PubMed citations: 6.

6 articles citing: Newt-omics: a comprehensive repository for omics data from the newt Notophthalmus viridescens

Comparative De Novo Transcriptome Assembly of Notophthalmus viridescens RNA-seq Data using Two Commercial Software Programs. PMID:30381788
Transcriptome analysis of newt lens regeneration reveals distinct gradients in gene expression patterns. PMID:23613853
Comparative RNA-seq analysis in the unsequenced axolotl: the oncogene burst highlights early gene expression in the blastema. PMID:23505351
A de novo assembly of the newt transcriptome combined with proteomic validation identifies new protein families expressed during tissue regeneration. PMID:23425577
What is it about 'eye of newt'? PMID:23425551
A microarray analysis of gene expression patterns during early phases of newt lens regeneration. PMID:23378727
http://dx.doi.org/10.1093/nar/GKR873

Tags:

Tags
More detailed information about this field from each metasource.

annotation
metasource: Fairsharing.org
version: FAIRsharing.org: Newt-omics; Newt-omics; DOI: https://doi.org/10.25504/FAIRsharing.k6a8e5; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

complementary dna
metasource: Fairsharing.org
version: FAIRsharing.org: Newt-omics; Newt-omics; DOI: https://doi.org/10.25504/FAIRsharing.k6a8e5; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

dna sequencing assay
metasource: Fairsharing.org
version: FAIRsharing.org: Newt-omics; Newt-omics; DOI: https://doi.org/10.25504/FAIRsharing.k6a8e5; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

gene ontology enrichment
metasource: Fairsharing.org
version: FAIRsharing.org: Newt-omics; Newt-omics; DOI: https://doi.org/10.25504/FAIRsharing.k6a8e5; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

peptide
metasource: Fairsharing.org
version: FAIRsharing.org: Newt-omics; Newt-omics; DOI: https://doi.org/10.25504/FAIRsharing.k6a8e5; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

protein identification
metasource: Fairsharing.org
version: FAIRsharing.org: Newt-omics; Newt-omics; DOI: https://doi.org/10.25504/FAIRsharing.k6a8e5; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

transcript
metasource: Fairsharing.org
version: FAIRsharing.org: Newt-omics; Newt-omics; DOI: https://doi.org/10.25504/FAIRsharing.k6a8e5; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

human and other vertebrate genomes
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

model organisms, comparative genomics
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

gene transcripts
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:22.439109

gene expression
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:22.439109

model organisms
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:22.439109

transcriptomics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:22.439109

complementary dna dna sequencing assay gene ontology enrichment peptide protein identification transcript human and other vertebrate genomes model organisms gene transcripts gene expression model organisms transcriptomics

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