Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

56 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Chromatin contact maps of 24 and 48 hours post-fertilisation zebrafish (Danio rerio) embryos and 48 hours post-fertilisation fibroblasts

ABSTRACT: In this experiment, we've examined chromatin conformation of zebrafish embryos at 24 and 48 hours post-fertilization (hpf), as well as 48 hpf fibroblasts. The aim of this study was to characterise the 3D chromatin structure of zebrafish and perform an evolutionary comparison with mammalian genomes (Homo sapiens and Mus musculus) focusing on syntenic regions and zebrafish ohnologs (duplicated genes that were kept in the genome after the third round of whole-genome duplication).

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Danio rerio

SUBMITTER: Benjamín Hernández-Rodríguez

PROVIDER: E-MTAB-6313 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Four Hi-C datasets from mESCs and 2C-like cells generated by knocking down the histone chaperone CAF-1 in mESCs

Project description:In this experiment, we've examined chromatin conformation of mESCs and 2C-like cells generated from a CAF-1 knockdown. The method to generate the knockdown was described in (). We performed a modified in situ Hi-C protocol from (Rao et al., 2014) and that can be found in detail at (Díaz et al., 2017, under revision). Samples were digested with MboI restriction enzyme having as starting material 100k cells with two biological replicates per sampling point. The aim of the experiment was to analyze the potential chromatin conformational changes that accompany the mESC to 2C-like transition.

2023-11-16 | E-MTAB-6330 | biostudies-arrayexpress

Six in situ Hi-C libraries of control and mESC auxin-inducible degrons for Scc1 and Ring1b.

Project description:In this experiment, we've examined chromatin conformation differences of E14 mESC against cohesin and Ring1b degrons. We performed a modified in situ Hi-C protocol from (Rao et al., 2014) that can be found in detail at (Díaz et al., 2018). Samples were digested with MboI restriction enzyme. The aim of the experiment was to characterize the role of cohesin and polycomb on the 3D structure of mouse chromatin.

2020-01-23 | E-MTAB-7816 | biostudies-arrayexpress

Low input Hi-C datasets for a diffuse large B-cell lymphoma sample, healthy control human B-cells and mouse embryonic stem cells

Project description:In this experiment, we've examined chromatin conformation of OG2 (B6; CBA-Tg(Pou5f1-EGFP)2Mnn/J; stock number 004654) mouse stem cells cultured as described in (Shi et al., 2008), using different amounts of starting cells. We performed a modified in situ Hi-C protocol for 6 samples digested with MboI restriction enzyme having as starting material 1 million (M), 100 thousand (k), 50k, 25k, 10k or 1k cells. As well as, to 2 samples digested with HindIII restriction enzyme that had as starting material 5M or 100k cells. Traditional in situ Hi-C protocols recommend 5-10 million starting cells. The aim of the experiment was to assess the impact of decreasing the cell number on reproducibility, library complexity, chromatin structure visualization in order to adapt the method to the study of rare cell populations. Furthermore, we have characterised the 3D structure of peripheral blood mononuclear cells (PBMCs) obtained from a blood extraction from a healthy donor and from a lymph node biopsy from a DLBCL patient as a proof of concept for the suitability of Low-C for rare cell population analysis.

2018-11-30 | E-MTAB-5875 | biostudies-arrayexpress

Three-dimensional folding and functional organization principles of the Drosophila genome

Project description:Chromosomes are the physical realization of genetic information and thus form the basis for its reading, hindering and propagation. Here we present a high-resolution chromosomal contact map derived from a new genome-wide chromosome conformation capture approach (a simplified version of the Hi-C method) applied to Drosophila embryonic nuclei. The data show that the entire genome is linearly partitioned into well-demarcated physical domains that overlap extensively with active and repressive epigenetic marks. Chromosomal contacts are hierarchically organized between domains. Global modeling of compaction and clustering of domains show that inactive domains are condensed and confined to their chromosomal territories, while active domains reach out of the territory to form remote intra- and inter-chromosomal contacts. One pilot sample, comprising seven paired-end Illumina GA-II lanes; one deep-sequenced sample, comprising seven paired-end Illumina HiSeq lanes

2012-01-20 | E-GEOD-34453 | biostudies-arrayexpress

In situ Hi-C study of chromatin conformation during early Drosophila development

Project description:In this experiment we examined higher order chromatin structure during early Drosophila melanogaster development. We performed in situ Hi-C for hand-sorted non-mitotic embryos at nuclear cycle number 12, 13 and 14, and for embryos at 3-4 hours post fertilisation. During this time in development, the zygotic genome is activated and zygotic transcription is taking place for the first time. To assess the impact of transcription on chromatin structure we injected the transcription inhibitors alpha-amanitin or triptolide before zygotic genome activation and performed Hi-C and ChIP-seq for RNA Pol II. Furthermore, we used Hi-C to study genome architecture in embryos lacking the transcription factor Zelda.

2017-04-06 | E-MTAB-4918 | biostudies-arrayexpress

CutnRun directed against O-GlcNac in the human DLD-1 cell line with doxycycline treatment to induce RNA Polymerase II degradation

Project description:This experiment aimed at investigating how O-GlcNac occupancy sites are impacted by RNA Polymerase II removal upon doxycycline stimulation. These human colon adenocarcinoma DLD-1 cells express OsTIR and a cassette encoding mini-AID (mAID) and fluorescent protein mClover (mAID+mClover) at the initiation site of the endogenous Rpb1 gene locus (POLR2A) (Nagashima 2019).

2024-08-31 | E-MTAB-14307 | biostudies-arrayexpress

HiC-sequencing in human monocyte differentiation (3D-MO)

Project description:This dataset consists of in situ HiC-seq data from human monocytes, monocyte-derived dendritic cells as well as monocyte-derived cells that were subjected to siRNA treatment targeting CTCF or RAD21. In total, the data set includes 42 samples.

2022-06-24 | E-MTAB-10848 | biostudies-arrayexpress

Hi-C of Drosophila embryos to investigate chromatin conformation during dorsal-ventral patterning

Project description:Hi-C was carried out for control embryos and embryos produced from gd7, Tollrm9/rm10, and Toll10B mutant mothers. The embryos from mutant mothers produce only a single type along the dorsal-ventral axis. We used these embryos to compare chromatin conformation across tissues.

2021-01-08 | E-MTAB-9306 | biostudies-arrayexpress

CutnRun of O-GlcNac in mouse ES cells in high glucose condition

Project description:Study of the chromatin occupancy of O-GlcNac in mouse ES cells cultivated in a high glucose concentration media

2024-08-31 | E-MTAB-14308 | biostudies-arrayexpress

CutnRun of O-GlcNac in mouse ES cells in low glucose condition at 6 hours, 8 hours, and 1 week

Project description:Study of the chromatin occupancy of O-GlcNac in mouse ES cells cultivated in low glucose condition at 6 hours, 8 hours, and 1 week

2024-08-31 | E-MTAB-14309 | 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