Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Jackson Drosophila astrocyte TRAP RNA-seq

PROVIDER: PRJNA354880 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR5052811.fastq.gz	Fastqsanger.gz
	SRR5052812.fastq.gz	Fastqsanger.gz
	SRR5052813.fastq.gz	Fastqsanger.gz
	SRR5052814.fastq.gz	Fastqsanger.gz

Items per page:

1 - 4 of 4

Similar Datasets

Transcriptional profiling of interneurons in the mouse prefrontal cortex

Project description:TRAP translational profiling is a method that allows investigators to genetically characterize specific cell types in complex tissues such as mouse brain. Using this technique we obtained RNA-Seq data from actively translating transcripts present in neurons in the prefrontal cortex of adult Crh-IRES-Cre mice (Jackson 012704). This work was supported by the Howard Hughes Medical Institute (N.H) and NIDA UG3-UH3 DA048385

2022-09-16 | GSE212780 | GEO

Cell type- and region-specific transcriptome of an MPTP-induced mouse model of Parkinson’s disease

Project description:Aiming to gain brain region- and cell type-specific resolution in gene expression profiling during PD pathogenesis, we applied the translating ribosome affinity purification (TRAP) technique to enrich the ribosome-bound mRNA of DaNs, microglia and astrocyte, for RNA-Seq and analysis in a mouse MPTP model of PD.

2022-10-15 | GSE213100 | GEO

RNA-seq of mouse cortical tissue and astrocytes after anesthesia and induction of neuronal activity

Project description:General anesthesia is a common clinical procedure yet can result in long term CNS-adverse effects, particularly in the elderly, or dementia patients. Suppression of cortical activity is a key feature of the anesthetic-induced unconscious state, with activity being a well-described regulator of pathways important for brain health. However the extent to which the effects of anesthesia go beyond simple suppression of neuronal activity is incompletely understood, as are its effects on non-neuronal cell types such as astrocytes, which are important integrators of both neuronal activity and inflammatory signalling. In order to address these questions, we performed a combination of RNA-seq and TRAP-seq (Translating Ribosome Affinity Purification, where astrocyte-specific translating mRNAs are sequenced) on mouse cortical tissue and primary cortical neurons.

2023-08-01 | E-MTAB-13054 | biostudies-arrayexpress

Reactive astrocytes with inflammatory signature in CCM disease in hypoxia and normoxia conditions

Project description:The CCM endothelium is hypersensitive to angiogenesis and can induce a hypoxic program associated with changes in angiogenesis, inflammation, and endothelial-cell metabolism under normoxic conditions. However, the role of active drivers of angiogenesis as CCM disease modifiers in human disease remains unclear. To assess whether CCM reactive astrocytes with neuroinflammatory capacity respond to hypoxia-induced CCM exacerbation, we employed the astrocyte-specific (Aldh1l1-EGFP/Rpl10a) Translational Ribosome Affinity Purification (TRAP) system in combination with a CCM mouse model (Pdcd10BECKO;Aldh1l1-EGFP/Rpl10a). TRAP protocol was performed using Slco1c1-iCreERT2;Pdcd10fl/fl;Aldh1l1-EGFP/Rpl10a mice to isolate ribosomes from astrocytes as previously described. Astrocyte-TRAP mRNAs were from cerebral tissue of mice age P50 exposed to hypoxia or normoxia conditions.

2024-09-23 | GSE236162 | GEO

Benchmarking differential expression, imputation and quantification methods for proteomics data

Project description:Data analysis is a critical part of quantitative proteomics studies in interpreting biological questions. Numerous computational tools including protein quantification, imputation, and differential expression (DE) analysis were generated in the past decade. However, searching optimized tools is still an unsolved issue. Moreover, due to the rapid development of RNA-Seq technology, a vast number of DE analysis methods are created. Applying these newly developed RNA-Seq-oriented tools to proteomics data is still a question that needs to be addressed. In order to benchmark these analysis methods, a proteomics dataset constituted the proteins derived from human, yeast, and drosophila with different ratios were generated. Based on this dataset, DE analysis tools (including array-based and RNA-Seq based), imputation algorithms, and protein quantification methods were compared and benchmarked. This study provided useful information on analyzing quantitative proteomics datasets. All the methods used in this study were integrated into Perseus which are available at https://www.maxquant.org/perseus.

2022-11-16 | PXD029891 | JPOST Repository

WT distal colon RNA-seq

Project description:To perform RNA-seq of distal colon tissue from WT mouse obtained from Jackson Laboratories

2023-08-01 | GSE229027 | GEO

Drosophila TRAP soma vs germline

Project description:Drosophila TRAP soma vs germline

| PRJNA961150 | ENA

Interrogating translating RNAs and cell-type specific gene expression using Cre-activated translating ribosome affinity purification

Project description:We characterize a Cre-activated TRAP allele (Rosa26fsTRAP) to show that endothelium-specific activation of Rosa26fsTRAP identifies endothelial cell enriched transcripts, and that cardiomyocyte-restricted TRAP is a useful means to identify genes that are differentially expressed in cardiomyocytes in a disease model. We also show that TRAP is an effective means to study translational regulation, and we several nuclear-encoded mitochondrial genes are under strong translational control. These RNA-seq data show that the TRAP strategy and the Rosa26fsTRAP allele will be useful tools to probe cell type specific transcriptomes, and to study translational regulation. Study TRAP RNA and total RNA in two cases: heart specific tissues, Banding or Sham, using RNA-seq technology.

2013-08-20 | E-GEOD-45152 | biostudies-arrayexpress

Integrative genome-wide analysis of dopaminergic neuron-specific PARIS expression dissects recognition of multiple PPAR-γ associated gene regulation (TRAP-Seq).

Project description:PURPOSE: The transcriptional repressor PARIS (ZNF746) was initially identified as a pathogenic co-substrate of PINK1 and parkin that leads to Parkinson’s disease (PD) by disrupting mitochondrial biogenesis through PPARγ coactivator -1α (PGC-1α) suppression. Later, accumulation of PARIS in dopamine (DA) neurons that cause neurotoxicity has been studied widely and growing evidence has linked defective mitochondrial biogenesis to PD pathogenesis. Yet, the mechanistic underpinnings of this link remain elusive. METHODS: We employed translating ribosome affinity purification (TRAP) followed by RNA sequencing (TRAP-seq) for transcriptome profiling of DA neurons in transgenic Drosophila lines we generated expressing human PARIS or human PARIS mutant (C571A). Together with TRAP control and whole brain samples, this data set is composed of a total of 10 (3, 3, 3, and 1 respectively) replicate samples representing 4 different treatment groups for a set of gene-level (a parametric F-test) and transcript-level (a Wald test or a likelihood ratio test) differential expression analysis. RESULTS: Firstly, we identified differentially expressed genes by human PARIS in fly DA neurons successfully. Then, we showed that PPARγ acts as a master regulator of transcriptomic changes induced by PARIS in the clusters of Drosophila dopaminergic neurons. Also, we validated this finding in human neuroblastoma cell line. CONCLUSION: PPARγ plays a crucial regulatory role in PARIS phenotype. Drosophila models of PARIS-induced neurodegeneration used in this work to represent PD phenotype and our TRAP-seq protocol serve as a paradigm for future studies to unravel mechanistic underpinnings of PARIS biology.

2021-08-02 | GSE175554 | GEO

Reprogramming of root cells during nitrogen-fixing symbiosis entails dynamic polysome association of coding and non-coding RNAs

Project description:we compared changes in the transcriptome and the translatome of M. truncatula roots upon rhizobial infection using direct RNA-seq and Translating Ribosome Affinity Purification (TRAP) combined with RNA-seq (TRAP-seq), respectively. TRAP is a ribosome immunopurification approach that has been extensively used in plants and mammals to assess translational changes

2019-11-15 | GSE133510 | 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