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View article: Genomic variations and epigenomic landscape of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel
Genomic variations and epigenomic landscape of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel Open
Background The teleost medaka ( Oryzias latipes ) is a well-established vertebrate model system, with a long history of genetic research, and multiple high-quality reference genomes available for several inbred strains. Medaka has a high t…
View article: The Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel
The Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel Open
Background Unraveling the relationship between genetic variation and phenotypic traits remains a fundamental challenge in biology. Mapping variants underlying complex traits while controlling for confounding environmental factors is often …
View article: Additional file 9 of Genomic variations and epigenomic landscape of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel
Additional file 9 of Genomic variations and epigenomic landscape of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel Open
Additional file 9: Table S7. Differentially-methylated regions. Genome coordinates of all significant differentially-methylated regions in 12 MIKK panel lines.
View article: Additional file 1 of Genomic variations and epigenomic landscape of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel
Additional file 1 of Genomic variations and epigenomic landscape of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel Open
Additional file 1: Table S1. Nanopore sequencing metrics. Metrics from ONT PromethION sequencing.
View article: Additional file 1 of The Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel
Additional file 1 of The Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel Open
Additional file 1: Table S1. MIKK panel lines. Table setting out all MIKK panel lines and the specific analyses each was included in.
View article: Additional file 2 of The Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel
Additional file 2 of The Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel Open
Additional file 2: Table S2. Fecundity data. Table with MIKK panel fecundity data.
View article: Additional file 4 of Genomic variations and epigenomic landscape of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel
Additional file 4 of Genomic variations and epigenomic landscape of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel Open
Additional file 4: Table S3. Graph segment alignments to reference genomes. Percentage of graph segments aligned to HdrR, HNI, and HSOK reference genomes. and shared across 12 MIKK panel lines.
View article: Additional file 7 of Genomic variations and epigenomic landscape of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel
Additional file 7 of Genomic variations and epigenomic landscape of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel Open
Additional file 7: Table S6. High-quality graph deletions. Genome coordinates for 16 MIKK panel-specific high quality graph deletions.
View article: Additional file 3 of The Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel
Additional file 3 of The Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel Open
Additional file 3: Table S3. Fish imaging parameters. Table with MIKK panel morphometric data.
View article: Additional file 6 of The Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel
Additional file 6 of The Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel Open
Additional file 6: Table S5. High confidence LoF variants. Table of homozygous high-confidence loss-of-function variants in the MIKK panel orthologous to a human dosage-sensitive gene.
View article: Additional file 3 of Genomic variations and epigenomic landscape of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel
Additional file 3 of Genomic variations and epigenomic landscape of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel Open
Additional file 3: Table S2. Individual assembly metrics. Metrics from individual assemblies including BUSCO, k-mer completeness, and QV measures.
View article: Additional file 5 of The Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel
Additional file 5 of The Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel Open
Additional file 5: Table S4. Variant types. Counts of short variants in each class based on predicted variant effect.
View article: Additional file 7 of The Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel
Additional file 7 of The Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel Open
Additional file 7: Table S6. eQTL SNPs. Significant eQTL SNPs with annotations.
View article: Additional file 5 of Genomic variations and epigenomic landscape of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel
Additional file 5 of Genomic variations and epigenomic landscape of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel Open
Additional file 5: Table S4. Graph segments shared across MIKK panel lines. Percentage of graph segments shared between the 12 MIKK panel lines.
View article: Additional file 6 of Genomic variations and epigenomic landscape of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel
Additional file 6 of Genomic variations and epigenomic landscape of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel Open
Additional file 6: Table S5. High-quality graph alternative paths. Genome coordinates for 19 MIKK panel-specific high-quality graph alternative paths.
View article: The Medaka Inbred Kiyosu-Karlsruhe (MIKK) Panel
The Medaka Inbred Kiyosu-Karlsruhe (MIKK) Panel Open
Unraveling the relationship between genetic variation and phenotypic traits remains a fundamental challenge in biology. Mapping variants underlying complex traits while controlling for confounding environmental factors is often problematic…
View article: Genomic variations and epigenomic landscape of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel
Genomic variations and epigenomic landscape of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel Open
The teleost medaka ( Oryzias latipes ) is a well-established vertebrate model system, with a long history of genetic research, and multiple high-quality reference genomes available for several inbred strains ( HdrR , HNI and HSOK ). Medaka…