Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome Analysis Reveals the Topography of Local Changes after Separate Transformations of the Same Reporter in Hundreds Loci of Yeast

ABSTRACT: "Position effect" means that the activity of an integrated reporter gene (IR) depends on its genomic location. Although the impact of local environment on IR (cis-effect of location) has been widely reported, the impact of IR integration on local environment and its potential mechanism (reaction of location), such as the change of expression landscape and its fitness are poorly understood. Here, we randomly selected ~250 previously constructed strains with GFP gene inserted into hundreds of different locations separately in yeast, and performed high-throughput transcriptome sequencing.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE142839 | GEO | 2020/02/21

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Transcriptome Analysis Reveals the Topography of Local Changes after Separate Transformations of the Same Reporter in Hundreds Loci of Yeast

Project description:Transcriptome Analysis Reveals the Topography of Local Changes after Separate Transformations of the Same Reporter in Hundreds Loci of Yeast

| PRJNA598580 | ENA

Propagation topography of redox phase transformations in heterogeneous layered oxide cathode materials.

Project description:Redox phase transformations are relevant to a number of metrics pertaining to the electrochemical performance of batteries. These phase transformations deviate from and are more complicated than the conventional theory of phase nucleation and propagation, owing to simultaneous changes of cationic and anionic valence states as well as the polycrystalline nature of battery materials. Herein, we propose an integrative approach of mapping valence states and constructing chemical topographies to investigate the redox phase transformation in polycrystalline layered oxide cathode materials under thermal abuse conditions. We discover that, in addition to the three-dimensional heterogeneous phase transformation, there is a mesoscale evolution of local valence curvatures in valence state topographies. The relative probability of negative and positive local valence curvatures alternates during the layered-to-spinel/rocksalt phase transformation. The implementation of our method can potentially provide a universal approach to study phase transformation behaviors in battery materials and beyond.

| S-EPMC6052144 | biostudies-literature

YTHDF2 inhibition potentiates radiotherapy by reprogramming suppressive myeloid cells [MeRIP-Seq]

Project description:RNA N6-methyladenosine (m6A) modification is implicated in cancer progression. However, the impact of m6A on the antitumor effects of radiotherapy and the related mechanisms are unknown. Here we show that ionizing radiation (IR) induces immunosuppressive myeloid-derived suppressor cell (MDSC) expansion and YTHDF2 expression in both murine models and humans. Following IR, loss of Ythdf2 in myeloid cells augments antitumor immunity and overcomes tumor radioresistance by altering MDSC differentiation and inhibiting MDSC infiltration and suppressive function. The remodeling of the landscape of MDSC populations by local IR is reversed by Ythdf2 deficiency. IR-induced YTHDF2 expression relies on NF-κB signaling; YTHDF2 in turn leads to NF-κB activation by directly binding and degrading transcripts encoding negative regulators of NF-κB signaling, resulting in an IR-YTHDF2-NF-κB circuit. Pharmacological inhibition of YTHDF2 overcomes MDSC-induced immunosuppression and improves combined IR and/or anti-PD-L1 treatment. Thus, YTHDF2 is a promising target to improve radiotherapy (RT) and RT/immunotherapy combinations.

2023-04-28 | GSE206384 | GEO

YTHDF2 inhibition potentiates radiotherapy by reprogramming suppressive myeloid cells [CITE-Seq]

2023-04-28 | GSE206381 | GEO

YTHDF2 inhibition potentiates radiotherapy by reprogramming suppressive myeloid cells [RIP-Seq]

2023-04-28 | GSE206379 | GEO

YTHDF2 inhibition potentiates radiotherapy by reprogramming suppressive myeloid cells [scRNA-Seq]

2023-04-28 | GSE206378 | GEO

Detecting metastatic tumors after γ-irradiation using longitudinal molecular imaging and gene expression profiling of metastatic tumor nodules

Project description:Microarray analysis in the mouse metastatic tumor after ɣ-irradiation(ɣ-IR): non-irradiated primary tumor vs. radiated primary tumor vs. metastatic tumor after ɣ-irradiation Metastatic tumors in C6-L (rat glioma cells ) xenografted mice were studied after local treatment with fractionated γ-IR. To accurately detect the metastatic nodules after γ-IR, we observed the effect of γ-IR on distant metastatic tumor growth. Metastatic nodules after γ-IR indicated extensive colonization of C6-L cells in the lungs within 6 weeks after γ-IR. Identified and described the molecular events occurring after γ-IR through gene expression profiling to elucidate genetic changes (differentially expressed genes between the γ-IR primary tumors vs. non-γ-IR primary tumors and metastatic lung nodules vs. γ-IR primary tumors). We investigated the change of gene expression profile in the γ-IR primary tumors vs. non-γ-IR primary tumors and metastatic lung nodules vs. γ-IR primary tumors in rat glioma (C6-L cell) xenograft model.

2015-09-18 | E-GEOD-73116 | biostudies-arrayexpress

Detecting metastatic tumors after γ-irradiation using longitudinal molecular imaging and gene expression profiling of metastatic tumor nodules

2015-09-18 | GSE73116 | GEO

Two separate quorum-sensing systems upregulate transcription of the same ABC transporter in Streptococcus pneumoniae.

Project description:Streptococcus pneumoniae secretes two different peptide pheromones used for intercellular communication. These peptides, which have completely unrelated primary structures, activate two separate signal transduction pathways, ComABCDE and BlpABCSRH, which regulate natural genetic transformation and bacteriocin production, respectively. Each signal transduction pathway contains a response regulator (ComE and BlpR, respectively) that activates transcription of target genes by binding to similar, but not identical, imperfect direct repeat motifs. In general the direct repeat binding sites are specific for one or the other of the two response regulators, ensuring that competence development and bacteriocin production are regulated separately. However, in the present study we show that the rate of transcription of an operon, encoding an ABC transporter of unknown function, can be stimulated by both peptide pheromones. We also show that this cross-induction is due to a hybrid direct repeat motif that can respond to both ComE and BlpR. To our knowledge this kind of convergent gene regulation by two separate two-component regulatory systems has not been described before in bacteria.

| S-EPMC400622 | biostudies-literature

Topography and evidence of a separate "fascia plate" for the femoral nerve inside the iliopsoas - A dorsal approach.

Project description:The femoral nerve stretch test is an essential part of clinical neurological examinations. This test is performed alongside Magnetic Resonance Imaging (MRI) to determine if there is any evidence of nerve root irritation, usually as a consequence of disc prolapse. The test occasionally gives false positive results. Why such false positives can occur, is subject to continued research, however, no obvious reason has yet emerged. We hypothesize that connectives of the femoral nerve may explain such a phenomenon. To see these connectives, we approached the femoral nerve from dorsal in 12 cases. With the use of ink injection into the subparaneural compartment of the femoral nerve and dissections, a thin transparent structure can clearly be seen that is separate from the epineurium, perineurium, and a paraneural sheath. A continuation of the paraneural sheath produces a fascia plate approximately 1.5 cm in width and with a thickness of around 3 mm, which not only circumnavigates the nerve but projects into the surrounding tissues. Our qualitative observations show that not only does this femoral nerve fascia plate exists, but it also contains nerves and vessels. Furthermore, we show that the femoral nerve is connected to the myofascial complex of the iliopsoas, and in a separate fascia plate from the iliopsoas fascia. This plate is a hitherto neglected connective which extends as far as the spinal dura mater. Evidence from our plastinates and histological sections suggests that when tension is applied to the femoral nerve during the femoral nerve stretch test, tension is also applied to the femoral nerve fascia plate. The femoral nerve fascia plate could be a specific factor that contributes to pain resulting in a false positive femoral nerve stretch test.

| S-EPMC8053587 | 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