Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Ribo-tag translatome analysis from Split-Cre transgenic mice

ABSTRACT: Ribo-tag translatome analysis from Split-Cre transgenic mice

PROVIDER: PRJNA657611 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR12463200_1.fastq.gz	Fastqsanger.gz
	SRR12463200_2.fastq.gz	Fastqsanger.gz
	SRR12463201_1.fastq.gz	Fastqsanger.gz
	SRR12463201_2.fastq.gz	Fastqsanger.gz
	SRR12463202_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 72

Similar Datasets

Ribo-tag translatome analysis from Split-Cre transgenic mice

Project description:We generated Split-Cre transgenic mice strains to target microglia or Lyve1+ macrophages in the brain. To obtain translatome from the each population, Split-Cre mice were crossed with Ribo-tag reporter mice, and translatome were acquired with anti-HA antibody immuno-percipitation.

2020-08-18 | GSE156368 | GEO

Next Generation translatome Sequencing (Ribo-seq) of Papillary Thyroid Carcinoma tissue sample and adjacent normal tissue

Project description:Through the translatome sequencing (Ribo-seq) of clinically obtained papillary thyroid carcinoma and its paired adjacent tissues, we tried to find the differences in the translation of various genes and evaluate the translation function of circular RNAs in the two tissues. We then performed gene expression profiling analysis using data obtained from Ribo-seq of 4 different pairs of Papillary Thyroid Carcinoma tissue sample and adjacent normal tissue. At the translatome level, we screened out 247 circRNAs with translation ability.

2024-08-01 | GSE212031 | GEO

Differential translatome in the DRG of mice treated with normal chow vs Western diet

Project description:We show differences in translatome of the DRG from ribo tagged mice fed normal chow or western diet.

2022-06-29 | GSE198895 | GEO

RNMT regulates the activated CD4 T cell transcriptome and translatome [Ribo-Seq]

Project description:RNMT regulates the activated CD4 T cell transcriptome and translatome [Ribo-Seq]

| PRJNA672952 | ENA

Translatome and transcriptome co-profiling reveals a role of TPRXs in human zygotic genome activation

Project description:Translational regulation plays a critical role during oocyte-to-embryo transition including zygotic genome activation. However, the translatome during OET and molecular mechanisms underlying human ZGA remain largely uncharted. Here, we integrated ultra-low-input Ribo-seq with RNA-seq (R2-lite) to jointly profile the translatome and transcriptome from the same samples across 8 stages in human oocytes and early embryos. These data not only unveil conservation and divergence of the translation landscapes between human and mouse OET, but also identify critical regulators of human ZGA.

2022-10-08 | GSE197265 | GEO

Intersectional Cre driver lines generated using split-intein mediated split-Cre reconstitution.

Project description:Tissue and cell type highly specific Cre drivers are very rare due to the fact that most genes or promoters used to direct Cre expressions are generally expressed in more than one tissues and/or in multiple cell types. We developed a split-intein based split-Cre system for highly efficient Cre-reconstitution through protein splicing. This split-intein-split-Cre system can be used to intersect the expression patterns of two genes or promoters to restrict full-length Cre reconstitution in their overlapping domains. To test this system in vivo, we selected several conserved human enhancers to drive the expression of either Cre-N-intein-N, or intein-C-Cre-C transgene in different brain regions. In all paired CreN/CreC transgenic mice, Cre-dependent reporter was efficiently induced specifically in the intersectional expression domains of two enhancers. This split-intein based method is simpler to implement compared with other strategies for generating highly-restricted intersectional Cre drivers to study complex tissues such as the nervous system.

| S-EPMC3390602 | biostudies-literature

Small proteome of Methanosarcina mazei: Insights from Ribo-seq and peptidomics under different nitrogen conditions

Project description:We used ribosome profiling (Ribo-seq) to generate a translatome map for the archaeon M. mazei under two growth conditions. The analysis of the datasets allowed to generate a high confidence inventory of small proteins in the model archaeon M. mazei and their regulation under nitrogen limiting conditions.

2024-08-08 | GSE240615 | GEO

Translatome analysis of brain endothelial cells in the acute epileptic mouse model

Project description:In this study, we provide the translatome data in the brain endothelial cells (BECs) of the adult cortex in response to acute neuronal activation by using translating ribosome affinity purification (TRAP) combined with high-throughput RNA sequencing analysis in Tie2-Cre:Ribo-Tag mice, which are designed for expressing hemagglutinin A (HA)-tagged RPL22, a ribosomal protein in endothelial cells depending on CRE recombinase. To increase neural activity rapidly, we adopted an acute epilepsy induction model in which pentylenetetrazol (PTZ), a GABAA receptor antagonist was injected and observed significant upregulation of c-fos-positive cells in the cortex. To obtain a high-quality BEC pool, we modified the TRAP method by adding the capillary isolation process before the immunoprecipitation step and finally verified BEC-specific translating mRNA purification using RT-PCR. We then analyzed RNA-seq data obtained from the BECs of cortex of adult mice injected with phosphate buffered saline (PBS) or PTZ and identified brain endothelial cell genes that are changed dynamically due to neuronal activation. This information will be useful for researchers to study neurovascular interaction or to identify biomarkers in epilepsy.

2023-04-26 | GSE173311 | GEO

Transcriptome and translatome of cardiomyocytes exposed to hypoxia in vivo and in vitro

Project description:Adult Cardiac hypoxia as a crucial pathogenesis factor can induce detrimental effects on cardiac injury and dysfunction. The global transcriptome and translatome reflecting the cellular response to hypoxia have not yet been extensively studied in myocardium. In this study, adult rats were subjected to acute normobaric hypoxia at 10% oxygen with 10 min (mild hypoxia) and 30 min (severe hypoxia). Rat H9C2 cardiomyocytes were treated with the culture condition (1% O2, 94% N2, and 5% CO2) for mild hypoxia (8 hr) and severe hypoxia(24 hr). We then conducted RNA-seq and Ribo-seq in non-infarcted left ventricular myocardial tissues and H9C2 cells exposed to different periods of hypoxia stress in vivo and in vitro.

2020-10-23 | E-MTAB-9541 | biostudies-arrayexpress

Split-Cre complementation restores combination activity on transgene excision in hair roots of transgenic tobacco.

Project description:The Cre/loxP system is increasingly exploited for genetic manipulation of DNA in vitro and in vivo. It was previously reported that inactive ''split-Cre'' fragments could restore Cre activity in transgenic mice when overlapping co-expression was controlled by two different promoters. In this study, we analyzed recombination activities of split-Cre proteins, and found that no recombinase activity was detected in the in vitro recombination reaction in which only the N-terminal domain (NCre) of split-Cre protein was expressed, whereas recombination activity was obtained when the C-terminal (CCre) or both NCre and CCre fragments were supplied. We have also determined the recombination efficiency of split-Cre proteins which were co-expressed in hair roots of transgenic tobacco. No Cre recombination event was observed in hair roots of transgenic tobacco when the NCre or CCre genes were expressed alone. In contrast, an efficient recombination event was found in transgenic hairy roots co-expressing both inactive split-Cre genes. Moreover, the restored recombination efficiency of split-Cre proteins fused with the nuclear localization sequence (NLS) was higher than that of intact Cre in transgenic lines. Thus, DNA recombination mediated by split-Cre proteins provides an alternative method for spatial and temporal regulation of gene expression in transgenic plants.

| S-EPMC4201524 | 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