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View article: Expanding the <i>BonnMu</i> sequence‐indexed repository of transposon induced maize (<i>Zea mays</i> L.) mutations in dent and flint germplasm
Expanding the <i>BonnMu</i> sequence‐indexed repository of transposon induced maize (<i>Zea mays</i> L.) mutations in dent and flint germplasm Open
SUMMARY The BonnMu resource is a transposon tagged mutant collection designed for functional genomics studies in maize. To expand this resource, we crossed an active Mutator ( Mu ) stock with dent (B73, Co125) and flint (DK105, EP1, and F7…
View article: NCBench: providing an open, reproducible, transparent, adaptable, and continuous benchmark approach for DNA-sequencing-based variant calling
NCBench: providing an open, reproducible, transparent, adaptable, and continuous benchmark approach for DNA-sequencing-based variant calling Open
We present the results of the human genomic small variant calling benchmarking initiative of the German Research Foundation (DFG) funded Next Generation Sequencing Competence Network (NGS-CN) and the German Human Genome-Phenome Archive (GH…
View article: Expanding the<i>BonnMu</i>sequence-indexed repository of transposon induced maize (<i>Zea mays</i>L.) mutations in dent and flint germplasm
Expanding the<i>BonnMu</i>sequence-indexed repository of transposon induced maize (<i>Zea mays</i>L.) mutations in dent and flint germplasm Open
The BonnMu resource is a transposon-tagged mutant collection designed for functional genomics studies in maize. To expand this resource, we crossed an active Mutator ( Mu ) line with dent (B73, Co125) and flint (DK105, EP1 and F7) germplas…
View article: Suberin deficiency and its effect on the transport physiology of young poplar roots
Suberin deficiency and its effect on the transport physiology of young poplar roots Open
Summary The precise functions of suberized apoplastic barriers in root water and nutrient transport physiology have not fully been elucidated. While lots of research has been performed with mutants of Arabidopsis , little to no data are av…
View article: Changes in wax composition but not amount enhance cuticular transpiration
Changes in wax composition but not amount enhance cuticular transpiration Open
This study focuses on the role of the qualitative leaf wax composition in modulating the cuticular water loss using a Populus × canescens cer6 mutant line, which accumulates C34–C46 wax ester dimers and is reduced in wax monomers >C24. The…
View article: NCBench: providing an open, reproducible, transparent, adaptable, and continuous benchmark approach for DNA-sequencing-based variant calling
NCBench: providing an open, reproducible, transparent, adaptable, and continuous benchmark approach for DNA-sequencing-based variant calling Open
We present the results of the human genomic small variant calling benchmarking initiative of the German Research Foundation (DFG) funded Next Generation Sequencing Competence Network (NGS-CN) and the German Human Genome-Phenome Archive (GH…
View article: Isolation and characterization of the gene <i>HvFAR1</i> encoding <scp>acyl‐CoA</scp> reductase from the <i>cer‐za.227</i> mutant of barley (<i>Hordeum vulgare</i>) and analysis of the cuticular barrier functions
Isolation and characterization of the gene <i>HvFAR1</i> encoding <span>acyl‐CoA</span> reductase from the <i>cer‐za.227</i> mutant of barley (<i>Hordeum vulgare</i>) and analysis of the cuticular barrier functions Open
Summary The cuticle is a protective layer covering aerial plant organs. We studied the function of waxes for the establishment of the cuticular barrier in barley ( Hordeum vulgare ). The barley eceriferum mutants cer‐za.227 and cer‐ye.267 …
View article: A2TEA: Identifying trait-specific evolutionary adaptations
A2TEA: Identifying trait-specific evolutionary adaptations Open
Background: Plants differ in their ability to cope with external stresses (e.g., drought tolerance). Genome duplications are an important mechanism to enable plant adaptation. This leads to characteristic footprints in the genome, such as …
View article: WES cropbioBonn WGGC CN 75M vcf results
WES cropbioBonn WGGC CN 75M vcf results Open
Whole Exome Sequencing Data Analysis with https://github.com/tgstoecker/WES_WGGC_2021_AG_Schoof HG001/NA12878 Agilent v6 2x101bp PE, NovaSeq 6000, 75M reads
View article: WES cropbioBonn WGGC CN Twist Exome vcf results
WES cropbioBonn WGGC CN Twist Exome vcf results Open
Whole Exome Sequencing Data Analysis with https://github.com/tgstoecker/WES_WGGC_2021_AG_Schoof HG001/NA12878 Twist Exome, NovaSeq 6000
View article: WES cropbioBonn WGGC CN Twist Exome vcf results
WES cropbioBonn WGGC CN Twist Exome vcf results Open
Whole Exome Sequencing Data Analysis with https://github.com/tgstoecker/WES_WGGC_2021_AG_Schoof HG001/NA12878 Twist Exome, NovaSeq 6000
View article: WES cropbioBonn WGGC CN 75M vcf results
WES cropbioBonn WGGC CN 75M vcf results Open
Whole Exome Sequencing Data Analysis with https://github.com/tgstoecker/WES_WGGC_2021_AG_Schoof HG001/NA12878 Agilent v6 2x101bp PE, NovaSeq 6000, 75M reads
View article: WES cropbioBonn WGGC CN Twist Exome vcf results
WES cropbioBonn WGGC CN Twist Exome vcf results Open
Whole Exome Sequencing Data Analysis with https://github.com/tgstoecker/WES_WGGC_2021_AG_Schoof HG001/NA12878 Twist Exome, NovaSeq 6000
View article: WES cropbioBonn WGGC CN 75M vcf results
WES cropbioBonn WGGC CN 75M vcf results Open
Whole Exome Sequencing Data Analysis with https://github.com/tgstoecker/WES_WGGC_2021_AG_Schoof HG001/NA12878 Agilent v6 2x101bp PE, NovaSeq 6000, 75M reads
View article: Transcriptome profiling at the transition to the reproductive stage uncovers stage and tissue-specific genes in wheat
Transcriptome profiling at the transition to the reproductive stage uncovers stage and tissue-specific genes in wheat Open
Background The transition from vegetative to floral phase is the result of complex crosstalk of exogenous and endogenous floral integrators. This critical physiological event is the response to environmental interaction, which causes bioch…
View article: Additional file 3 of Transcriptome profiling at the transition to the reproductive stage uncovers stage and tissue-specific genes in wheat
Additional file 3 of Transcriptome profiling at the transition to the reproductive stage uncovers stage and tissue-specific genes in wheat Open
Additional file 3: Table S2. List of primers used for PCR, RT-qPCR and sequencing of candidate genes.
View article: Additional file 5 of Transcriptome profiling at the transition to the reproductive stage uncovers stage and tissue-specific genes in wheat
Additional file 5 of Transcriptome profiling at the transition to the reproductive stage uncovers stage and tissue-specific genes in wheat Open
Additional file 5: Table S4. List of the total annotated and mapped transcripts differentially expressed in SAM in 18 libraries.
View article: Additional file 2 of Transcriptome profiling at the transition to the reproductive stage uncovers stage and tissue-specific genes in wheat
Additional file 2 of Transcriptome profiling at the transition to the reproductive stage uncovers stage and tissue-specific genes in wheat Open
Additional file 2: Table S1. List of significant QTL for heading in the Germany adapted cultivars.
View article: Additional file 9 of Transcriptome profiling at the transition to the reproductive stage uncovers stage and tissue-specific genes in wheat
Additional file 9 of Transcriptome profiling at the transition to the reproductive stage uncovers stage and tissue-specific genes in wheat Open
Additional file 9: Table S8. Gene ontology enrichment analysis in “Kontrast” relatively to “Basalt” in SAM.
View article: Additional file 4 of Transcriptome profiling at the transition to the reproductive stage uncovers stage and tissue-specific genes in wheat
Additional file 4 of Transcriptome profiling at the transition to the reproductive stage uncovers stage and tissue-specific genes in wheat Open
Additional file 4: Table S3. Paired Student t-test of significant Waddington scores difference between cultivars.
View article: Additional file 10 of Transcriptome profiling at the transition to the reproductive stage uncovers stage and tissue-specific genes in wheat
Additional file 10 of Transcriptome profiling at the transition to the reproductive stage uncovers stage and tissue-specific genes in wheat Open
Additional file 10: Table S9. Gene ontology enrichment analysis in “Kontrast” relatively to “Basalt” in the leaves.
View article: Additional file 6 of Transcriptome profiling at the transition to the reproductive stage uncovers stage and tissue-specific genes in wheat
Additional file 6 of Transcriptome profiling at the transition to the reproductive stage uncovers stage and tissue-specific genes in wheat Open
Additional file 6: Table S5. List of the total annotated and mapped transcripts differentially expressed in leaves in 18 libraries.
View article: Additional file 7 of Transcriptome profiling at the transition to the reproductive stage uncovers stage and tissue-specific genes in wheat
Additional file 7 of Transcriptome profiling at the transition to the reproductive stage uncovers stage and tissue-specific genes in wheat Open
Additional file 7: Table S6. Differential expressed genes in “Kontrast” compared to “Basalt” mapped in the QTL intervals in SAM.
View article: Additional file 8 of Transcriptome profiling at the transition to the reproductive stage uncovers stage and tissue-specific genes in wheat
Additional file 8 of Transcriptome profiling at the transition to the reproductive stage uncovers stage and tissue-specific genes in wheat Open
Additional file 8: Table S7. Differential expressed genes in “Kontrast” compared to “Basalt” mapped in the QTL intervals in the leaves.
View article: A2TEA: Identifying trait-specific evolutionary adaptations
A2TEA: Identifying trait-specific evolutionary adaptations Open
Background: Plants differ in their ability to cope with external stresses (e.g., drought tolerance). Genome duplications are an important mechanism to enable plant adaptation. This leads to characteristic footprints in the genome, such as …
View article: A2TEA.Workflow test data
A2TEA.Workflow test data Open
Test data for https://github.com/tgstoecker/A2TEA.Workflow
View article: A2TEA.Workflow test data
A2TEA.Workflow test data Open
Test data for https://github.com/tgstoecker/A2TEA.Workflow
View article: A2TEA Brassicaceae example data
A2TEA Brassicaceae example data Open
Example result object of A2TEA.Workflow output investigating drought stress in Brassicaceae species.
View article: A2TEA Brassicaceae example data
A2TEA Brassicaceae example data Open
Example result object of A2TEA.Workflow output investigating drought stress in Brassicaceae species.
View article: A2TEA.Workflow Poaceae reduced example data
A2TEA.Workflow Poaceae reduced example data Open
Example result object of A2TEA.Workflow output investigating drought stress in Poaceae species. Input for the workflow was reduced: Peptide FASTA files were reduced to 2000 proteins; the transcriptomic data is subsampled to 2M reads to all…