Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Assembly of the Arabidopsis (Col-0) centromeres using Oxford Nanopore Technology long-read DNA sequencing.

ABSTRACT: Nanopore long-read sequencing was used to generate a complete assembly of the Arabidopsis centromeres.

INSTRUMENT(S): MinION

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Todd Michael

PROVIDER: E-MTAB-10272 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Whole exome sequencing grid of untreated, TPA-treated, and DMBA+TPA-treated mouse back skin

Project description:We generated meso-scale grids from mouse back skin by collecting paired whole-exome sequencing (WES) and bulk RNA sequencing (bulk RNA), retaining coordinate information to preserve spatial context across the grids. Grids were derived from untreated mice (UN, n = 4), mice treated with the cell-cycle activator TPA for twelve weeks (TO, n = 3), and mice treated with the carcinogen DMBA followed by repeated TPA until the first visible papilloma (DT, n = 3). Cumulatively, we collected 690 bulk RNA and 476 WES samples, the majority of which are paired. All DT animals developed papillomas, whereas no macroscopic skin alterations were observed in UN or TO mice.

2026-06-11 | E-MTAB-15745 | biostudies-arrayexpress

Translation profiling of fission yeast wild type and rng3-65 fission yeast to identify changes in th enumber of ribosomes associated with specific transcripts

Project description:Genome-wide translational profiling of rng3-65 compared to wild type cells. We used sucrose gradients to separate RNAs according to the number of associated ribosomes (a surrogate for translational efficiency). Preparation of the extracts and fractionation was carried out as described in Lackner et al, 2007 (Mol Cell 26(1):145-55). The fractions were pooled into four groups (1 closest to the top, i.e. not associated with ribosomes and 4 closest to the bottom, i.e., associated with polysomes). RNA was extracted from the pools and the corresponding pools from wild type and mutant cells were directly compared using DNA microarrays. Changes in translation are expected to alter the number of ribosomes associated with specific transcripts, and therefore result in a redistribution of the RNAs across the different fractions.

2008-12-23 | E-TABM-565 | biostudies-arrayexpress

H3K27ac ChIPseq of the ecDNA-positive colon cancer cell line COLO 320DM with and without hydroxyurea treatment

Project description:Extrachromosomal DNA (ecDNA) is a major driver of oncogene amplification, intratumoural heterogeneity and rapid genetic change. We observe that ecDNA frequently undergoes segregation errors and is incorporated into micronuclei (MN) in ecDNA positive cancer cells. Different ecDNA species can coalesce into MN and lead to asymmetric inheritance. EcDNA in MN undergoes epigenetic changes and shows decreased oncogene transcription. Cells harbouring ecDNA-positive MN show prolonged cell cycle progression and an increased likelihood of cell death. Here we assess ecDNA H3K27ac occupancy after hydroxyurea treatment. COLO 320DM cells were treated with 80 µM hydroxyurea or DMSO (vehicle control) for 3 days and fixed for ChIPseq library preperation.

2026-07-02 | E-MTAB-16944 | biostudies-arrayexpress

RNA-seq of zebrafish embryos with mutations in a muscle-specific kinase and the giant titin protein

Project description:RNA-seq of zebrafish embryos with mutations in srpk3 (sa1890 allele) and/or ttn.1 (sa5562 allele). Each of the 24 samples (six samples for each of four genotypes) represents RNA from a pool of three 5 dpf zebrafish embryos.

2024-02-09 | E-MTAB-12934 | biostudies-arrayexpress

RNA-seq of e.coli under growth, regulated growth arrest and disrupted growth arrests - second repetition

Project description:Compares the transcriptomes of E.Coli under natural or unnatural nutrient depletions, leading to either regulated or disrupted growth arrests respectively. E.coli are grown in minimal media with supplemented 0.1% AA. regulated growth arrest (\\"CASP\\"): cultures are grown to stationary phase and sampled after 24 hours in growth arrest. disrupted growth arrest (\\"Disrupted\\"): cultures are grown to ~0.1OD (exponential growth) at which point SHX is added to the growth media. Cultures arrest their growth. Samples are collected 24 hours after growth arrest. Growth conditions (\\"Exponential\\"): cultures are collected just before adding SHX.

2025-07-01 | E-MTAB-14332 | biostudies-arrayexpress

ChIP-Seq of Cluster situated regulators (ForJ, ForF and ForZ) of the formicamycin BGC in Streptomyces formicae

Project description:ForJ, ForF and ForZ are cluster situated regulators of the formicamycin biosynthetic gene cluster in Streptomyces forimcae. This ChIP Sequencing experiment was conducted to identify where in the genome these regulators bind in order to identify which transcripts they might regulate.

2019-05-31 | E-MTAB-8006 | biostudies-arrayexpress

Brewer - M.muscuclus - NOX4 TG

Project description:Transcriptomic analysis of cardiomyocytes in NOX4 transgenic mice

2014-06-01 | E-MEXP-3161 | biostudies-arrayexpress

RNA-seq of Caenorhabditis elegans (at Late L4 stage) of rrf-3(pk1426);rde-1(ne219);unc-62p::rde-1 and daf-2(e1370);rrf-3(pk1426);rde-1(ne219);unc-62p::rde-1 grown on control RNAi or cyd-1 RNAi.

Project description:To check cyd-1-dependent gene expression changes in different genetic backgrounds. We have collected the synchronized late L4 worms and isolated the total RNA and performed mRNA sequencing.

2024-10-14 | E-MTAB-13172 | biostudies-arrayexpress

RNA-seq of Caenorhabditis elegans at Late L4 stage of WT, daf-2(e1370), daf-16(mgDf50);daf-2(e1370) on control RNAi and cdk-12 RNAi

Project description:To check cdk-12 and DAF-16 dependent gene expression change in different genetic backgrounds. We have collected the synchronized late L4 worms and isolated the total RNA and did the mRNA sequencing.

2023-08-25 | E-MTAB-11189 | biostudies-arrayexpress

3C-seq analysis of Acinetobacter baumannii AB5075 in the presence and absence of H-NS-39

Project description:The experiment contains 3C-seq data for Acinetobacter baumannii strain AB5075 with different genetic alterations. The strain was grown at 37 degrees in LB medium and nucleoprotein was cross-linked using formaldehyde. Genomic DNA was isolated and digested with NlaIII before being ligated with T4 ligase. Sequencing was then used to identify junctions between ligated DNA sequences.

2024-07-15 | E-MTAB-13800 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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