Ontology highlight
ABSTRACT:
PROVIDER: PRJEB43089 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| CAJNOX01.dat.gz | Other | |||
| CAJNOX01.fasta.gz | Fasta.gz | |||
| CAJNOX01.master.dat | Other | |||
| CAJNOZ01.dat.gz | Other |
Items per page: 5 1 - 5 of 49 |
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Project description:Nanopore DNA-sequencing of medaka brain samples from the MIKK panel
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Project description:High coverage Illumina DNA-sequencing of brain samples across all MIKK panel lines
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Project description:We used the nanopore Cas9 targeted sequencing (nCATS) strategy to specifically sequence 125 L1HS-containing loci in parallel and measure their DNA methylation levels using nanopore long-read sequencing. Each targeted locus is sequenced at high coverage (~45X) with unambiguously mapped reads spanning the entire L1 element, as well as its flanking sequences over several kilobases. The genome-wide profile of L1 methylation was also assessed by bs-ATLAS-seq in the same cell lines (E-MTAB-10895).
2023-09-22 | E-MTAB-12247 | biostudies-arrayexpress
Project description:Medaka fish is a long standing genetic model organism from the 1930s. Uniquely amongstvertebrates Medaka fish can be routinely inbred from the wild (laboratory mice are inbred, butthis does not happen as a routine process from wild individuals), leading to a large number offully inbred wild-derived strains. As part of a broader collaboration I am part of a project toinbred over 100 wild derived strains of Medaka and use them in a similar manner toArabidopsis and Drosophila wild derived lines.To help explore the phenotyping possibilities in this context, we have taken alreadyestablished wild Medaka lines and done reciprocal F1 crosses between 3 strains, and have 4tissues, and a number of parental tissues, giving a total of 40 samples. By doing RNA-seq onthese tissues we do a number of things:(a) assess the level of allele specific expression in Medaka(b) test whether there is any imprinting (parent of origin) in fish. This is thought to not be thecase, but in fact has not been well tested (not least because getting truly inbred fish is hard)(c) assess the level of random allelic activation in brain(d) assess the feasibility for RNAseq based phenotyping in Medaka, providing preliminarydata for future proposals.This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
2015-12-08 | E-ERAD-390 | biostudies-arrayexpress
Project description:During development, the inherited DNA methylation patterns from the parental gametes needs to be remodeled into a state compatible with embryonic pluripotency. In Zebrafish, this remodeling is achieved by the maternal methylome becoming hypomethylated to match the paternal methylome. However, how this is achieved in medaka (another teleost fish) is currently not known. Moreover, how DNA methylation remodeling is impacted in hybrid organisms, and the effects this may have on their development, is also not known. Here we address these questions by generation whole genome bisulfite sequencing data for zebrafish, medaka and zebrafish medaka embryos.
2023-08-25 | E-MTAB-12535 | biostudies-arrayexpress
Project description:We have improved the DamID method to make it applicable for vertebrate life specimens. We use iDamID-seq to profile the binding profile of the transcription factor Rx2 in medaka embryos at stage 22 of development. We compare two replicates of the fusion Dam-Rx2 against two replicates of the fusion Dam-GFP as control. Medaka embryos at 1-cell stage were injected with mRNA transcribed in vitro from one of the two Dam fusions. The embryos were allowed to grow in normal conditions up to stage 22. The genomic DNA was isolated and treated to extract only the DpnI fragments that had adenine methylation. These fragments were subjected to deep sequencing.
2016-10-06 | E-MTAB-4610 | biostudies-arrayexpress
Project description:We used bs-ATLAS-seq to comprehensively map the genomic location and assess the DNA methylation status of human full-length LINE-1 elements (L1) in the genome of 2102Ep cells (E-MTAB-10895). We also achieved targeted nanopore sequencing to assay DNA methylation over a subset of loci (E-MTAB-12247). To further study the link between L1 DNA methylation and expression, we performed, in the same cell line, RNA-seq (E-MTAB-12246), as well as YY1 and H3K4me3 ChIP-seq (this dataset).
2023-09-23 | E-MTAB-12249 | biostudies-arrayexpress
Project description:The involvement of miRNAs during vertebrate oogenesis is poorly documented. Based on the assumption that ovarian-specific or ovarian-predominant genes usually play important roles during oogenesis, we searched for ovarian-predominant miRNAs in the medaka (Oryzias latipes) ovary. 10 tissus were collected from adult medaka (intestine, ovary, testis, liver, heart, gills, kidney, brain, muscle and bone) and RNAs were hybridized on a designed agilent microarray displaying 3800 distinct miRNAs from different teleost and vertebrate species. We identified 66 miRNAs sequences predominantly expressed in the ovary that had never been previously described in medaka.
2016-08-31 | GSE80823 | GEO