Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Ribotag-based Next Generation Sequencing of tumor-associated astrocytes

ABSTRACT: Ribotag-based Next Generation Sequencing of tumor-associated astrocytes

PROVIDER: PRJNA796542 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR17576000_1.fastq.gz	Fastqsanger.gz
	SRR17576000_2.fastq.gz	Fastqsanger.gz
	SRR17576001_1.fastq.gz	Fastqsanger.gz
	SRR17576001_2.fastq.gz	Fastqsanger.gz
	SRR17576002_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 64

Similar Datasets

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and AXL-/- astrocytes Transcriptomes

Project description:Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare Wild Type astrocytes transcriptome profiling (RNA-seq) to AXL-/- astrocytes transcriptome profiling and to explore the mechanism by which AXL interferes with type I IFN signaling in WT astrocytes. We performed an RNA-Seq analysis of WT and AXL-/- U-251MG cells in the absence of ZIKV. Surprisingly, the intrinsic level of type I IFN signaling was lower in AXL-/- cells than in WT cells. This result was further confirmed by RT-qPCR

2017-11-06 | GSE106545 | GEO

Ribotag-based Next Generation Sequencing of tumor-associated astrocytes

Project description:GfapCRE:Rpl22HA mice were intracranially implanted with GL261 glioma cells (GBM) or injected with PBS (sham). Seventeen days later, RNA was retrieved from mouse brain extract (input) by anti-HA immunoprecipitation

2022-07-11 | GSE193526 | GEO

Epigenome signatures during gastric carcinogenesis based on next generation sequencing

Project description:Epigenome signatures during gastric carcinogenesis based on next generation sequencing

| PRJNA238870 | ENA

Genome-wide analysis of the transcriptional profile of astrocytes across EAE by CNS region in Gfap-Cre;Ribotag(f/f) mice uisng Ribotag immunoprecipitation.

Project description:We identify pathways regulated in astrocytes across EAE by CNS region. Multiple sclerosis (MS) is an autoimmune neurologic disease leading to demyelination and neurologic dysfunction controlled by both genetic and environmental factors. In addition to CNS-infiltrating immune cells, CNS-resident cells, such as astrocytes, are thought to play an important role in MS pathogenesis. However, a comprehensive understanding of the extent to which gene expression is disrupted in astrocytes is not known. Here, we implement single-cell RNA sequencing, in vivo genetic perturbations, cell-specific RNA profiling by Ribotag, as well as single-cell RNA sequencing of human MS patient samples to identify a transcriptional regulatory network in astrocytes that controls the pathogenesis of EAE and potentially, MS. We defined an astrocyte subpopulation characterized by expression of the small Maf protein, MAFG, which represses NRF2-driven antioxidant mechanisms and promotes EAE pathogenesis. Mechanistically, MAFG suppresses NRF2-dependent antioxidant genetic programs by cooperating with its cofactor, MAT2a, to promote DNA methylation in the context of CNS inflammation, which in turn increases pathogenic signaling processes in astrocytes. MAFG/MAT2a astrocytes are controlled by GM-CSF signaling, which drives EAE pathogenesis and MAFG expression. MAFG is activated in astrocytes derived from MS patients, which are characterized by DNA methylation programs, pro-inflammatory signaling processes including GM-CSF signaling, and repressed NRF2 activation. Together, these data create a transcriptional and epigenetic framework to analyze CNS inflammation in MS and may provide new therapeutic targets.

2020-02-12 | GSE130118 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and AXL-/- astrocytes Transcriptomes

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and AXL-/- astrocytes Transcriptomes

| PRJNA417188 | ENA

Diagnosis of Lynch Syndrome Based on Next-generation Sequencing in Colorectal Cancer

Project description:The purpose of this study is to determine the proportion of patients diagnosed with Lynch syndrome in colorectal cancer patients with the loss of staining by immunohistochemistry (IHC) of any of the mismatch repair (MMR) proteins. Besides, this study aims to test the specificity and the sensitivity of detecting microsatellite instability (MSI) by next-generation sequencing, and to find out the consistency between IHC and MSI in colorectal cancer patients in China. In addition, researchers want to analyze the clinical characteristics and germline mutation of Lynch syndrome in Chinese population.

| 2236244 | ecrin-mdr-crc

Next generation sequence analysis

Project description:Next generation sequence analysis

| PRJNA560769 | ENA

Next Generation Sequencing-based mRNA sequencing of human adipose mesenchymal stem cells

Project description:Next Generation Sequencing-based mRNA sequencing of human adipose mesenchymal stem cells

| PRJNA667748 | ENA

Next-generation RNA sequencing of human astrocyte cultures to study the comparative levels of transmembrane proteins and their transcriptional variants

Project description:The aim of this study was to perform Next-generation RNA sequencing to analyse the expression of transmembrane proteins in human astrocytes and compare the prevalance of transcriptional variants thereof.

2023-05-25 | GSE228084 | GEO

Re-evaluating Microglia Expression Profiles Using RiboTag and Cell Isolation Strategies

Project description:Transcriptome profiling is widely used to infer functional states of specific cell types, as well as their responses to stimuli, to define contributions to physiology and pathophysiology. Focusing on microglia, the brain macrophages, we report here a side-by-side comparison of classical cell sort-based transcriptome sequencing and the ‘RiboTag’ method that avoids cell retrieval from tissue context and yields translatome sequencing information. Conventional whole cell microglia transcriptomes were found to be significantly tainted by artifacts induced by tissue-dissociation, cargo contaminations and transcripts sequestered from ribosomes. Conversely, our data highlight the added value of RiboTag profiling to assess the accuracy of Cre transgenic mice. Collectively, this study indicates method-based biases, reveals observer effects and establishes RiboTag-based translatome profiling as a valuable complement to standard sort-based profiling strategies.

2018-05-04 | GSE114001 | 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