Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Timing of Germ Layer Initiation Linked to Spatially Patterned Onset of Genome Activation

ABSTRACT: Timing of Germ Layer Initiation Linked to Spatially Patterned Onset of Genome Activation

PROVIDER: PRJNA833390 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR18969100_1.fastq.gz	Fastqsanger.gz
	SRR18969100_2.fastq.gz	Fastqsanger.gz
	SRR18969200_1.fastq.gz	Fastqsanger.gz
	SRR18969200_2.fastq.gz	Fastqsanger.gz
	SRR18969101_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 536

Similar Datasets

Timing of Germ Layer Initiation Linked to Spatially Patterned Onset of Genome Activation

Project description:This SuperSeries is composed of the SubSeries listed below.

2022-08-22 | GSE201874 | GEO

Spatially patterned scaffolds enhances vascular organization and functional integration in volumetrc muscle loss

Project description:Spatially patterned scaffolds enhances vascular organization and functional integration in volumetrc muscle loss

| PRJNA524279 | ENA

Spatially patterned scaffolds enhances vascular organization and functional integration in volumetrc muscle loss

Project description:We report the application of bioengineered skeletal muscle composed of murine skeletal myoblasts interspersed with human vascular endothelial cells (ECs) using spatially patterned scaffolds for the treatment of volumetric muscle loss. To gain insights into the molecular mechanisms by which spatial patterning promoted myo-angiogenesis, we performed mRNA sequencing of engineered muscle and endothelialized engineered muscle on either randomly-oriented or aligned scaffolds. The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) from four groups: 1) randomly-oriented scaffold seeded with myoblasts; 2) randomly-oriented scaffolds seeded with myoblasts + ECs; 3) aligned scaffold seeded with myoblasts only; 4) aligned scaffold seeded with myoblasts + ECs. Samples were generated in triplicate and the NovaSeq 6000 (Illumina) sequencing platform was utilized. 150-bp paired-end reads were generated (20-30 million reads per sample). The raw data were checked for quality with FastQC (Version 0.11.7) and results were aggregated with MultiQC and were aligned to the mouse genome (GRCm38) using STAR (Version 2.5.3a) with ENCODE options for long RNA-seq pipeline. The alignment results were assessed using Samtools and aggregated with MultiQC (Version 1.5) and the differential gene expression analysis of the uniquely mapped reads/raw counts wwas performed using the DESeq2 package (Version 1.20.0). Each DE analysis was composed of a pairwise comparison between an experimental group and the control group. Differentially expressed genes were identified after false discovery rate (FDR = 0.05) correction.

2019-04-01 | GSE127171 | GEO

Phenotype modulation of VSMCs on patterned substrate

Project description:Loss of contractility and acquisition of an epithelial phenotype of vascular smooth muscle cells (VSMCs) are key events in proliferative vascular pathologies such as atherosclerosis and post-angioplastic restenosis. There is no proper cell culture system allowing VSMC differentiation so that it is difficult to delineate the molecular mechanism responsible for proliferative vasculopathy. We investigated whether a micro-patterned substrate could restore the contractile phenotype of VSMCs in vitro. To induce and maintain the differentiated VSMC phenotype in vitro, we introduced a micro-patterned groove substrate to modulate the morphology and function of VSMCs.

2013-11-14 | E-MTAB-1888 | biostudies-arrayexpress

Rif1 regulates the replication timing domains on the human genome

Project description:DNA replication is spatially and temporally regulated during S-phase. DNA replication timing is established in early G1-phase at a point referred to as TDP (timing decision point). We show that Rif1 (Rap1-interacting-factor1), originally identified as a telomere binding factor in yeast, is a critical determinant of the replication timing program in human cells. Depletion of Rif1 results in specific loss of mid-S replication foci profiles, stimulation of initiation events in early S-phase and changes in long-range replication timing domain structures. Overall replication timing is shifted toward mid-S in both directions, suggesting that replication timing regulation is abrogated in the absence of Rif1. Rif1 tightly binds to nuclear insoluble structures at late-M to early-G1 and regulates the chromatin-loop sizes. Furthermore, Rif1 colocalizes specifically with the mid-S replication foci. Thus, Rif1 establishes the mid-S replication domains that are restrained from being activated at early S-phase. Our results indicate that Rif1 plays crucial roles in determining the replication timing domain structures through regulating higher-order chromatin architecture. HeLa cells (ATCC), with a total of 4 individual replicates

2012-05-14 | E-GEOD-37971 | biostudies-arrayexpress

mRNA Initiation and Termination are Spatially Coordinated

Project description:mRNA Initiation and Termination are Spatially Coordinated

| PRJNA1252147 | ENA

mRNA Initiation and Termination are Spatially Coordinated

Project description:mRNA Initiation and Termination are Spatially Coordinated

| PRJNA1252142 | ENA

Spatially-patterned and functional kidney assembloids recapitulate progenitor self-assembly and enable high-fidelity in vivo disease modeling

Project description:Spatially-patterned and functional kidney assembloids recapitulate progenitor self-assembly and enable high-fidelity in vivo disease modeling

| PRJNA1102884 | ENA

Spatially-patterned and functional kidney assembloids recapitulate progenitor self-assembly and enable high-fidelity in vivo disease modeling

Project description:Spatially-patterned and functional kidney assembloids recapitulate progenitor self-assembly and enable high-fidelity in vivo disease modeling

| PRJNA1091627 | ENA

Spatially-patterned and functional kidney assembloids recapitulate progenitor self-assembly and enable high-fidelity in vivo disease modeling

Project description:Spatially-patterned and functional kidney assembloids recapitulate progenitor self-assembly and enable high-fidelity in vivo disease modeling

| PRJNA1138241 | ENA

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