Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Permissive epigenomic states endow reprogramming competence to a broad range of transcriptional regulators

ABSTRACT: Permissive epigenomic states endow reprogramming competence to a broad range of transcriptional regulators

PROVIDER: PRJNA627156 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR11580502_1.fastq.gz	Fastqsanger.gz
	SRR11580502_2.fastq.gz	Fastqsanger.gz
	SRR11580503_1.fastq.gz	Fastqsanger.gz
	SRR11580503_2.fastq.gz	Fastqsanger.gz
	SRR11580504_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 24

Similar Datasets

Permissive epigenomic states endow reprogramming competence to a broad range of transcriptional regulators

Project description:Identifying molecular targets that regulate reprogramming competence of transcription factors in donor cells broadens our understanding of reprogramming process. Here, by a chemical screen targeting major epigenetic pathways in human reprogramming, we discovered that inhibiting specific epigenetic roadblocks allows iPSC generation with almost all OCT factors. Amongst these epigenetic pathways was not only DOT1L-mediated H3K79 methylation but also other modifications catalyzed by LSD1, DNMTs and HDACs, and we found that simultaneous inhibition of these pathways not only dramatically enhances reprogramming competence of most OCT factors but in fact enables to dismantle species-dependent reprograming competence of OCT6, NR5A1, NR5A2, TET1 and GATA3. Harnessing these permissive epigenetic states, we performed an additional screen with 98 transcriptional regulators. Thereby, we identified 25 novel genes that can functionally replace OCT4 in inducing pluripotency. Our findings provide a conceptional framework for understanding how transcription factors elicit reprogramming in dependency of the donor cell epigenome that differs across species.

2020-06-24 | GSE149017 | GEO

Sequence of the broad host-range IncP-alpha plasmid pRK404G

Project description:Re-sequencing of the broad host-range IncP-alpha plasmid pRK404

| PRJEB36160 | ENA

Title: A siRNA targets and inhibits a broad range of SARS-CoV-2 infections including Delta variant

Project description:a broad range of SARS-CoV-2 inhibitor

| PRJEB50508 | ENA

A model that cancer cells’ metastatic competence is determined by their states

Project description:A polyclonal mouse model of breast tumor heterogeneity using model cell line 4T1 was developed previously. It was shown that 4T1 cells were composed of mixed subpopulations with specializations, including dominating the primary tumor, contributing to metastatic populations, etc. Here in a different angle, we reveal that each 4T1 cells can switch between 2 distinct states, which could be easily misclassified into 2 subpopulations, as the 2 states can be distinguished by distinct patterns of gene expression, dramatic difference of metastatic competence, stem-cell like feature or not, etc. The event for each 4T1 cell to exhibit one state or another is stochastic and the metastatic competence of clones generated from a single 4T1 cell is variable rather than stable. Further, given that metastatic competence of 4T1 cells is not stable, classification of clones based on metastatic competence is highly biased. Similarly, the classification of 4T1 clones based on gene expression profiles is also highly biased. Taken together, our data support that the exhibition of metastatic competence depends on the state of 4T1 cells and do not support the existence of subpopulations with specialization. To the best of our knowledge, no similar work has ever been reported.

2018-03-20 | GSE112038 | GEO

Circuitry rewiring directly couples competence to predation in the gut-dweller Streptococcus salivarius

Project description:Small distortions in transcriptional networks might lead to drastic phenotypical changes, especially in cellular developmental programs such as competence for natural transformation. Here, we report a pervasive circuitry rewiring for competence and predation interplay in commensal streptococci. Canonically, in model species of streptococci such as Streptococcus pneumoniae and Streptococcus mutans, the pheromone-based two-component system BlpRH is a central node that orchestrates the production of antimicrobial compounds (bacteriocins) and incorporates signal from the competence activation cascade. However, the human commensal Streptococcus salivarius does not contain a functional BlpRH pair and in this species, the competence signaling system ComRS directly couples bacteriocin production and competence commitment. This network shortcut might account for an optimal reaction against microbial competitors and could explain the high prevalence of S. salivarius in the human digestive tract. Moreover, the broad spectrum of bacteriocin activity against pathogenic bacteria showcases the commensal and genetically tractable S. salivarius species as a user-friendly model for natural transformation and bacterial predation.

2018-01-10 | GSE100416 | GEO

Transcriptome analysis of the broad-host range pathogen Pythium myriotylum during infection of ginger (Zingiberis officinale) leaves.

Project description:Oomycetes, such as the broad host-range necrotrophic plant pathogen Pythium myriotylum, cause devastating crop losses. We have previously identified P. myriotylum as the major pathogen infecting ginger (Zingiber officinale) rhizomes in China with symptoms of Pythium soft rot (PSR) disease. Ginger is an important crop with global production estimated at approximately three million metric tonnes with about 20% of this production in China. To better understand how P. myriotylum infects ginger, transcriptomic analysis was performed on two P. myriotylum isolates (SWQ7 and SL2) infecting ginger leaves. From both of the isolates, there was a clear separation between the transcriptome replicates from the mycelial control condition and those from the infection of the ginger leaf. In SWQ7 and SL2, there were 2,110 and 2,513 genes upregulated during infection of ginger, respectively. Of the putative effectors, a subset of the NEP1-like toxin protein (NLP) effectors were highly induced during the infection of ginger leaves. Insights from the transcriptome highlight the important role of a subset of plant cell wall degrading enzymes (PCWDEs) and effectors in the pathogenicity of P. myriotylum towards ginger. The surprisingly large numbers of P. myriotylum PCWDEs and effectors within the genome may be due to the broad host-range of P. myriotylum whereby particular subsets of the PCWDEs and effectors are required for pathogenicity towards particular hosts.

2022-07-22 | GSE174557 | GEO

Microglia P2Y6 receptor signaling regulates a broad range of innate immune responses after TLR engagement

Project description:Microglia P2Y6 receptor signaling regulates a broad range of innate immune responses after TLR engagement

| PRJNA802378 | ENA

Host Factors with Reduced Expression in Two HCV Permissive Cell Lines as Compared to the Non-Permissive Parent Cell Line Huh7

Project description:Drugs directly targeting Hepatitis C (HCV) are often rendered useless by the high mutation rate of the virus. Thus, we deduce that targeting of host factor that affect HCV replication may provide enhanced therapy fort HCV infection. Hepatocyte cell line Huh7 is known to be non-permissive for Hepatits C (HCV) replication. Through a method developed by the Rice laboratory (Blight, K.J., et al., J Virol, 2002), selection of a small subset of permissive hepatocytes is possible. The Rice laboratory generated the first permissive cell line, Huh7.5, using this method. We generated another permissive cell line, HRP1, using the same method. With microarray, we compared the expression of host mRNAs in non-permissive Huh7 to both Huh7.5 and HRP1 searching for host factors lost in the cell lines permisive for HCV replication. Non-permissive cell line Huh7 and permissive cell lines Huh7.5 and HRP1 were harvested for RNA extraction and hybridization on Affymetrix microarrays.

2011-05-01 | E-GEOD-25156 | biostudies-arrayexpress

Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia

Project description:Injury induces retinal Muller glia of non-mammalian, but not mammalian, vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia, we used bulk and single-cell RNA-seq and ATAC-seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish, chick and mice. This was conducted during glial development, following inner and outer retinal injury, as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data, together with functional analysis of candidate genes, identified evolutionarily conserved and species-specific gene regulatory networks controlling glial quiescence, gliosis, and neurogenic competence. In zebrafish and chick, transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence, while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell-based therapies aimed at restoring retinal neurons lost to disease.

2020-05-01 | GSE135406 | GEO

Single-cell RNA-sequencing of breast cancer cells growing in invasion permissive and non-permissive 3D matrices

Project description:Murine breast cancer organoids (MMTV-PyMT) were embeded in basement membrane extract (BME, invasion non-permissive) or collagen I (invasion-permissive). Organoids were harvested after 5days for single-cell RNA-sequencing (SORT-seq).

2022-12-13 | GSE197821 | GEO

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