Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide maps of m6dA bases in drosophila ovary genomic DNA

ABSTRACT: We report the m6dA modification on the Drosophila genome. We collected ovary genomic DNA from 2-day wild-type and DMAD mutant files and performed DNA-immunoprecipitation(DNA-IP)experiments using anti-m6dA antibody. The generated DNA library was subjected to a high-throughput deep sequencing analysis. In this assay, the IgG-immunoprecipited DNA from the same amount of wild-type ovaries was used as the control, and the high-throughput sequencing resulted in a range of approximately 3 to 4.6 million reads. In sum, we identified 50 and 195 peaks from wild-type and DMAD mutant samples. Importantly, m6dA is mainly utilized to modify the transposon sequence on the chromosomes.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE64340 | GEO | 2016/06/01

SECONDARY ACCESSION(S): PRJNA270771

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Genome-wide maps of m6dA bases in drosophila ovary genomic DNA

Project description:We report the m6dA modification on the Drosophila genome. We collected ovary genomic DNA from 2-day wild-type and DMAD mutant files and performed DNA-immunoprecipitation(DNA-IP)experiments using anti-m6dA antibody. The generated DNA library was subjected to a high-throughput deep sequencing analysis. In this assay, the IgG-immunoprecipited DNA from the same amount of wild-type ovaries was used as the control, and the high-throughput sequencing resulted in a range of approximately 3 to 4.6 million reads. In sum, we identified 50 and 195 peaks from wild-type and DMAD mutant samples. Importantly, m6dA is mainly utilized to modify the transposon sequence on the chromosomes. Examination of m6dA modifications in Genomic DNA of WT and DMAD mutant ovary.

2016-06-01 | E-GEOD-64340 | biostudies-arrayexpress

Genomic Analysis of Relapsed Pediatric Acute Lymphoblastic Leukemia

Project description:<p>Although multi-agent combination chemotherapy is curative in a significant fraction of childhood acute lymphoblastic leukemia (ALL) patients, 20% of cases relapse and most die due to chemo-refractory disease. Here we used whole-exome and whole-genome sequencing to analyze the mutational landscape and pattern of clonal evolution at relapse in pediatric ALL cases. These analyses showed that ALL relapses originate from a common ancestral precursor clone of the diagnosis and relapsed populations and frequently harbor mutations implicated in chemotherapy resistance. RAS-MAPK pathway activating mutations in NRAS, KRAS and PTPN11 were present in 24/55 (44%) cases in our series. Notably, while some cases showed emergence of RAS mutant clones at relapse, in others, RAS mutant clones present at diagnosis were replaced by RAS wild type populations. Mechanistically, functional dissection of mouse and human wild type Kras and mutant Kras (Kras G12D) isogenic leukemia cells demonstrated induction of methotrexate resistance, but also improved response to vincristine, in mutant Kras- expressing lymphoblasts. These results identify chemotherapy driven selection as a central mechanism of leukemia clonal evolution and pave the road for the development of tailored personalized therapies for the treatment of relapsed ALL. </p>

| phs001072 | dbGaP

High-throughput sequencing of zebrafish wild-type and duox mutant larvae

Project description:High-throughput sequencing of zebrafish wild-type and duox mutant larvae

| PRJNA604591 | ENA

Transcriptome-wide RNA 5-methylcytosine methylation in roots of Arabidopsis thaliana

Project description:Here we use bisulfite conversion of rRNA depleted RNA combined with high-throughput Illumina sequencing (RBS-seq) to identify single-nucleotide resolution of m5C sites transcriptome-wide in Arabidopsis thaliana roots. m5C sites were analyzed in wild type (WT) and an Arabidopsis T-DNA KO mutant for the RNA methyltransferase TRM4B.

2017-04-07 | GSE80052 | GEO

High-throughput deep sequence of zebrafish wild-type and ezh2 mutant embryos

Project description:High-throughput deep sequence of zebrafish wild-type and ezh2 mutant embryos

| PRJNA407886 | ENA

Expression profiling of palatal shelves in Tbx1 mutant mice

Project description:To assess the influence of Tbx1 on gene expression profile within the developing palate we performed a microarray screen using RNA isolated from dissected secondary palate shelves of E13.5 wild type, Tbx1+/- and Tbx1-/- mice. Significant differences were identified between genotypes, with a total of 67 genes demonstrating at least a 2-fold change (p<0.05) in expression. These were clustered into 5 groups, including those downregulated in mutant compared to wild type and heterozygote (n=36); those progressively downregulated from wild type to mutant (n=12); those upregulated in heterozygote and downregulated in mutant compared to wild type (n=2); those progressively upregulated from wild type to mutant (n=12) and those downregulated in heterozygote and upregulated in mutant compared to wild type (n=5). High-throughput real time quantitative RT-PCR confirmed a total of 18 genes significantly changed between wild type and mutant and 24 between heterozygote and mutant. Amongst these, 15 were present in both groups and all except 1 were downregulated in the mutant. There were no significant differences in gene expression between wild type and heterozygous palatal shelves.

2013-04-02 | GSE37904 | GEO

Transcriptome analysis of mouse preimplantation embryos when DNA damage checkpoint is perturbed

Project description:To investigate the importance of DNA damage checkpoint regulation in mammalian preimplantation embryos, we overexpressed wild type and mutant form of CHK1 kinase in mouse zygotes and performed high-throughput RNA-sequencing of zygotes, late 2-cell embryos and blastocysts. Transcriptome analysis revealed that zygotes are particular sensitive to the perturbation of Chk1 governed DNA damage checkpoint. However, once zygotes can overcome DNA damage checkpoint induced cell cycle arrest, they can still have normal development.

2021-05-04 | GSE163765 | GEO

HeLa/16E6-16E7 Cells (Wild-type E2-infected vs. Mutant E2-infected)

Project description:HeLa/16E6-16E7 cells after expression of wild-type E2 compared to an E2 DNA-binding mutant Keywords: Wild-type E2 Infection vs. Mutant E2 Infection

2007-01-24 | GSE6760 | GEO

UVDE-seq mapping of UV-induced 6-4PPs and atypical TA photoproducts

Project description:We used a novel high-throughput sequencing method known as UVDE-seq to map the formation of UV-induced 6-4 photoproducts (6-4PP) and atypical thymidine-adenine (TA) photoproducts at single nucleotide resolution across the yeast genome in wild-type and rad16 mutant cells, which are deficient in GG-NER. We also analyzed 6-4PP and TA photoproducts in UV-irradiated yeast genomic DNA (i.e., naked DNA).

2023-02-28 | GSE190471 | GEO

LC-MS/MS analysis of maize seedling leaf bases

Project description:1 g samples of maize seedling leaf bases were collected from the wild-type (Zheng58) plants and the mutants (bzu3-2). we undertook glycoproteomics analyses of the N-glycans. Based on the libraries of maize protein group and plant N-glycosylation modification in the Uniprot database, we identified 2,194 intact N-glycopeptides, and quantified 181 differentially expressed intact N-glycopeptides (DEGPs)

2023-07-24 | PXD041642 | Pride

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