Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

PRO-seq, ATAC-seq, and Pol II ChIP-seq in 20 hour sea urchin embryos

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Strongylocentrotus purpuratus

PROVIDER: GSE160463 | GEO | 2021/06/03

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

PRO-seq, ATAC-seq, and Pol II ChIP-seq in 20 hour sea urchin embryos (PRO-Seq)

Project description:PRO-seq, ATAC-seq, and Pol II ChIP-seq signals are used to predict active developmental enhancers.

2021-06-03 | GSE160460 | GEO

PRO-seq, ATAC-seq, and Pol II ChIP-seq in 20 hour sea urchin embryos (ATAC-Seq)

Project description:PRO-seq, ATAC-seq, and Pol II ChIP-seq signals are used to predict active developmental enhancers.

2021-06-03 | GSE160461 | GEO

PRO-seq, ATAC-seq, and Pol II ChIP-seq in 20 hour sea urchin embryos (ChIP-seq)

Project description:PRO-seq, ATAC-seq, and Pol II ChIP-seq signals are used to predict active developmental enhancers.

2021-06-03 | GSE160462 | GEO

PRO-seq, ATAC-seq, and Pol II ChIP-seq in 20 hour sea urchin embryos

Project description:PRO-seq, ATAC-seq, and Pol II ChIP-seq in 20 hour sea urchin embryos

| PRJNA673234 | ENA

PRO-seq, ATAC-seq, and Pol II ChIP-seq in 20 hour sea urchin embryos (PRO-Seq)

Project description:PRO-seq, ATAC-seq, and Pol II ChIP-seq in 20 hour sea urchin embryos (PRO-Seq)

| PRJNA673237 | ENA

PRO-seq, ATAC-seq, and Pol II ChIP-seq in 20 hour sea urchin embryos (ATAC-Seq)

Project description:PRO-seq, ATAC-seq, and Pol II ChIP-seq in 20 hour sea urchin embryos (ATAC-Seq)

| PRJNA673239 | ENA

PRO-seq, ATAC-seq, and Pol II ChIP-seq in 20 hour sea urchin embryos (ChIP-seq)

Project description:PRO-seq, ATAC-seq, and Pol II ChIP-seq in 20 hour sea urchin embryos (ChIP-seq)

| PRJNA673238 | ENA

PRO-IP-seq tracks molecular modifications of engaged Pol II complexes at nucleotide resolution.

Project description:RNA Polymerase II (Pol II) is a multi-subunit complex that undergoes covalent modifications as transcription proceeds through genes and enhancers. Rate-limiting steps of transcription control Pol II recruitment, site and degree of initiation, pausing duration, productive elongation, nascent transcript processing, transcription termination, and Pol II recycling. Here, we develop Precision Run-On coupled to Immuno-Precipitation sequencing (PRO-IP-seq), which double-selects nascent RNAs and transcription complexes, and track phosphorylation of Pol II C-terminal domain (CTD) at nucleotide-resolution. We uncover precise positional control of Pol II CTD phosphorylation as transcription proceeds from the initiating nucleotide (+1 nt), through early (+18 to +30 nt) and late (+31 to +60 nt) promoter-proximal pause, and into productive elongation. Pol II CTD is predominantly unphosphorylated from initiation until the early pause-region, whereas serine-2- and serine-5-phosphorylations are preferentially deposited in the later pause-region. Upon pause-release, serine-7-phosphorylation rapidly increases and dominates over the region where Pol II assembles elongation factors and accelerates to its full elongational speed. Interestingly, tracking CTD modifications upon heat-induced transcriptional reprogramming demonstrates that Pol II with phosphorylated CTD remains paused on thousands of heat-repressed genes. These results uncover dynamic Pol II regulation at rate-limiting steps of transcription and provide a nucleotide-resolution technique for tracking composition of engaged transcription complexes.

| S-EPMC10624850 | biostudies-literature

Ethanol-treated Lytechinus variegatus (sea urchin) embryos

Project description:The effects of ethanol on developmental gene expression in sea urchins is compared to controls at three time points during gastrulation.

2022-06-28 | GSE207100 | GEO

Pantropic retroviruses as a transduction tool for sea urchin embryos.

Project description:Sea urchins are an important model for experiments at the intersection of development and systems biology, and technical innovations that enhance the utility of this model are of great value. This study explores pantropic retroviruses as a transduction tool for sea urchin embryos, and demonstrates that pantropic retroviruses infect sea urchin embryos with high efficiency and genomically integrate at a copy number of one per cell. We successfully used a self-inactivation strategy to both insert a sea urchin-specific enhancer and disrupt the endogenous viral enhancer. The resulting self-inactivating viruses drive global and persistent gene expression, consistent with genomic integration during the first cell cycle. Together, these data provide substantial proof of principle for transduction technology in sea urchin embryos.

| S-EPMC3325703 | biostudies-literature

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