Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Unraveling the whole genome DNA methylation profile of zebrafish kidney marrow through Oxford Nanopore sequencing

ABSTRACT: Zebrafish is a widely used model organism for investigating human diseases, including hematopoietic disorders. However, a comprehensive methylation baseline for zebrafish primary hematopoietic organ, the kidney marrow (KM), is still lacking. We employed Oxford Nanopore Technologies (ONT) sequencing to profile DNA methylation in zebrafish KM by generating four KM datasets, with two groups based on the presence or absence of red blood cells. Our findings revealed that blood contamination in the KM samples reduced read quality and altered methylation patterns. Compared with whole-genome bisulfite sequencing (WGBS), the ONT-based methylation profiling can cover more CpG sites (92.4% vs 70%-80%), and exhibit less GC bias with more even genomic coverage. And the ONT methylation calling results showed a high correlation with WGBS results when using shared sites. This study establishes a comprehensive methylation profile for zebrafish KM, paving the way for further investigations into epigenetic regulation and the development of targeted therapies for hematopoietic disorders.

ORGANISM(S): Danio rerio

PROVIDER: GSE232842 | GEO | 2023/05/19

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

scRNA-seq of kidney marrow cells from Gata2b deficient and wild type zebrafish

Project description:GATA2 is a pivotal hematopoietic transcription factor required for generation and maintenance of hematopoietic stem cells (HSCs). Due to early embryonic lethality of Gata2 deficiency in mice, its role during adult hematopoiesis is incompletely understood. In zebrafish, mammalian functions of Gata2 are split between two orthologues: Gata2a and Gata2b. Previous studies have shown that Gata2b is prominently expressed in hematopoietic stem and progenitor cells (HSPCs), whereas Gata2a is mainly expressed in the vasculature. We found that Gata2b deficient zebrafish have a reduction in embryonic definitive HSPC numbers and have impaired myeloid lineage differentiation, but are viable. This allowed us to study the role of Gata2b in adult hematopoiesis. To assess the impact of Gata2b deficiency on the transcriptional profile of HSPCs and differentiated cells, we sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow (KM) of WT and germline Gata2b deficient zebrafish based on scatter profiles and processed for single-cell RNA sequencing. To enrich the scarce HSC population, we used pooled KM from two WT and Gata2b deficient Tg(CD41:GFP) zebrafish per sample and included all CD41:GFPlow expressing cells present in the kidney marrow pool as these cells were shown to contain transplantable HSCs.

2022-04-09 | E-MTAB-10370 | biostudies-arrayexpress

Pore-C: Combination of chromatin capture assay and Oxford Nanopore Technology long read sequencing.

Project description:Higher-order chromatin structure arises from the combinatorial physical interactions of many genomic loci. To investigate this aspect of genome architecture we developed Pore-C, which couples chromatin conformation capture with Oxford Nanopore Technologies (ONT) long reads to directly sequence multi-way chromatin contacts without amplification.

2022-05-12 | GSE149117 | GEO

RNA-seq and RRBS of developing zebrafish larval brain and WGBS of 4 week old WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain

Project description:DNA methylation predominantly occurs at CG dinucleotides in vertebrate genomes, however, non-CG methylation (mCH) is also detectable in vertebrate tissues, most notably in the nervous system. In mammalian brains, it is well established that: i) mCH is targeted to CAC trinucleotides by DNMT3A, ii) enriched in gene bodies and repetitive elements, and iii) associated with transcriptional repression. However, the possible conservation of these mCH features in zebrafish is largely unexplored and has yet to be functionally demonstrated. In this study, we analyse the transcriptomes (RNA-seq) and methylome (RRBS) of developing zebrafish larvae (1-6 weeks) and adult brain (6 month). We additionally elucidate a role for dnmt3aa/dnmt3ab in mCH deposition via CRISP/CAS9 KO and WGBS of 4 week old brains

2020-12-18 | E-MTAB-9924 | biostudies-arrayexpress

Whole Genome Bisulfite Sequencing of Female Zebrafish Embryos Treated with Atrazine

Project description:We exposed zebrafish embryos to 0.3, 3, and 30 ppb (µg/L) of ATZ for 72 hours post fertilization. We performed whole-genome bisulfite sequencing (WGBS) to assess the effects of developmental ATZ exposure on DNA methylation in female fish brains

2020-01-24 | GSE144154 | GEO

Detecting cell-of-origin and cancer-specific methylation features of cell-free DNA from Nanopore sequencing

Project description:The Oxford Nanopore (ONT) platform provides portable and rapid genome sequencing, and its ability to natively profile DNA methylation without complex sample processing is attractive for clinical sequencing. We recently demonstrated ONT shallow whole-genome sequencing to detect copy number alterations (CNA) from the circulating tumor DNA (ctDNA) of cancer patients. Here, we show that cell-type and cancer-specific methylation changes can also be detected, as well as cancer-associated fragmentation signatures. This feasibility study suggests that ONT shallow WGS could be a powerful tool for liquid biopsy, especially real-time medical applications.

2022-04-27 | GSE185307 | GEO

Nanopore RNA-seq of polyA+ RNA from HAP1 and HEK293 cell lines

Project description:Sequencing was performed to assess the ability of Nanopore direct cDNA and native RNA sequencing to characterise human transcriptomes. Total RNA was extracted from either HAP1 or HEK293 cells, and the polyA+ fraction isolated using oligodT dynabeads. Libraries were prepared using Oxford Nanopore Technologies (ONT) kits according to manufacturers instructions. Samples were then sequenced on ONT R9.4 flow cells to generate fast5 raw reads in the ONT MinKNOW software. Fast5 reads were then base-called using the ONT Albacore software to generate Fastq reads.

2019-03-14 | E-MTAB-7778 | biostudies-arrayexpress

Human Cortical DNA methylation by WGBS in Autism Spectrum Disorders and Rett Syndrome

Project description:Human Cortical DNA methylation by WGBS in Autism Spectrum Disorders and Rett Syndrome

| PRJNA490887 | ENA

Single-cell RNA-seq (10x Chromium V3) of zebrafish csf1ra and csf1rb mutant whole kidney marrows

Project description:Macrophage colony-stimulating factor receptor (M-CSFR/CSF1R) signaling is crucial for the differentiation, proliferation, and survival of myeloid cells. Therapeutic targeting of the CSF1R pathway is a promising strategy in many human diseases, including neurological disorders or cancer. Zebrafish are commonly used for human disease modeling and preclinical therapeutic screening. Therefore, it is necessary to understand the proper function of cytokine signaling in zebrafish to reliably model human-related diseases. Here, we investigate the roles of zebrafish csf1ra and csf1rb in adult myelopoiesis using single-cell RNA sequencing. Our analysis of adult whole kidney marrow (WKM) hematopoietic cells suggests that csf1rb is expressed mainly by blood and myeloid progenitors and that the expression of csf1ra and csf1rb is non-overlapping. We point out differentially expressed genes important in hematopoietic cell differentiation and immune response in selected WKM populations. Our findings could improve the understanding of myeloid cell function and lead to the further study of CSF1R pathway deregulation in disease, mostly in cancerogenesis.

2021-04-24 | E-MTAB-10360 | biostudies-arrayexpress

Methylated DNA is over-represented in whole-genome bisulfite sequencing data

Project description:The development of whole-genome bisulfite sequencing (WGBS) has led to a number of exciting discoveries about how genomes utilize DNA methylation and has led to a plethora of novel testable hypotheses. Methods for constructing sodium bisulfite-converted and amplified libraries have recently excelled to the point that the bottleneck for experiments that use WGBS has shifted to data analysis and interpretation. Here we present empirical evidence for an over-representation of methylated DNA from WGBS. This enrichment for methylated DNA is exacerbated by higher cycles of PCR and is influenced by the type of uracil-insensitive DNA polymerase used for amplifying the sequencing library. Future efforts to computationally correct for this enrichment bias will be essential to increasing the accuracy of determining methylation levels for individual cytosines. MethylC-Seq of Arabidopsis thaliana

2014-09-11 | E-GEOD-58217 | biostudies-arrayexpress

Whole Genome Bisulfite Sequencing of Autism and Control Human BA9 Cortex

Project description:Autism spectrum disorders (ASD), characterized by lack of social and communicative behaviors, have complex etiologies involving multiple genetic and environmental risk factors. Epigenetic information, such as brain DNA methylation patterns, is predicted to reveal insight into the gene networks, cell types, and developmental timing of ASD etiology, but prior methylation studies in ASD have been limited by platform or data integration. Here, we used whole genome bisulfite sequencing (WGBS) to examine DNA methylation genome wide in Brodmann Area 9 of dorsal lateral prefrontal cortex of ASD and Control samples.

2019-09-17 | GSE109875 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data