Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Sciatic nerve crush upregulation of B2-SINE expression at specific genomic loci

ABSTRACT: Sciatic nerve crush upregulation of B2-SINE expression at specific genomic loci

PROVIDER: PRJNA962457 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR24322422_1.fastq.gz	Fastqsanger.gz
	SRR24322422_2.fastq.gz	Fastqsanger.gz
	SRR24322423_1.fastq.gz	Fastqsanger.gz
	SRR24322423_2.fastq.gz	Fastqsanger.gz
	SRR24322424_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 32

Similar Datasets

Sciatic nerve crush upregulation of B2-SINE expression at specific genomic loci

Project description:To map the loci of B2-SINE expressed in DRG which are regulated by sciatic nerve injury, paired-end RNAseq was carried on DRG neurons following sciatic nerve injury at 24h and 72h (3d) after injury. Mice were subjected to crush of the sciatic nerve in one side, while the other nerve was spared and used as naive control condition.

2025-05-16 | GSE230720 | GEO

Analysis of the interactome of B2-SINE RNA transcripts

Project description:B2-SINEs are noncoding RNAs which are transcribed by RNA polymerase III (Pol III) from short interspersed nuclear elements (SINEs), which are high copy number transposable elements in the mouse genome. Unexpectedly have observed significant induction of non-coding RNAs from the B2-SINE subclass of repeat element RNAs in DRG neurons following sciatic nerve injury. We next sought to identify intracellular targets of GI-SINEs, by protein pull-down from sciatic nerve axoplasm using biotinylated B2-SINE RNA as bait. We generated two constructs from the B2 consensus sequence, comprising 5’ (1-75nt) and 3’ (75-166nt) sequences, both predicted to retain their respective structures, and used the constructs to pull down axoplasm proteins for mass spectrometry analysis. Further confirmatory experiments were performed using the mentioned -175nt sequence vs a control U1 SL3+4 RNA

2025-05-05 | PXD060976 | Pride

Targeting GI-SINE (Growth inducing B2-SINE) RNA in DRG neurons by Antisense Oligonucleotides (ASO)

Project description:We identified 2 specific motifs that are enriched in GI-SINE RNA expressed in sciatic-nerve injured DRG neurons compared to non-regulated B2-SINE RNAs. We designed a mix of 5 ASOs (21nt phosphorothioate DNA with LNA-flanks) that target these motifs and transfected those into cultured dorsal root ganglia (DRG) neurons. Control ASO was based on a 21nt non-targetting sequence from shControl backbone (addgene plasmid #85741). Primary DRG neurons were transfected using Dharmafect-4 with ASO at 50nM final concentration 1 hour after plating. Cultures were processed for RNA extraction 48h after transfection for RNA sequencing to identify changes in B2-SINE expression.

2025-05-16 | GSE262153 | GEO

Sciatic nerve crush regulation of RNA alternative poly-adenylation

Project description:Poly-adenylation regulates post-transcriptional processing and localization of mRNA. To study the effect of nerve injury on poly-adenylation across the transcriptome, 3'-end RNAseq was carried on DRG neurons following sciatic nerve injury. Mice were subjected to crush of the sciatic nerve in one side, while the other nerve was spared and used as naive control condition.

2025-05-16 | GSE230721 | GEO

Role of ATF3 in the transcription of GI-SINEs (growth inducing B2-SINEs) in DRG neurons in response to sciatic nerve crush

Project description:Injury of the sciatic nerve upregulates a specific subset of B2-SINE RNAs in Dorsal Root Ganglia (DRG) neurons that enhances axon regeneration, which we termed GI-SINEs (growth inducing SINEs). Based on ATAC-seq and transcription factor binding site analysis and in-culture perturbation of AP-1 TFs, we hypotheiszed that GI-SINEs specifically regulated by injury activated AP-1 TFs. Here we experimentally tested the role of ATF3, a CREB TF that belongs to the AP-1 TF superfamily, in the transcriptional upregulation of GI-SINEs. ATF3 was previously identified and characterized as a key activator of nerve-injury induced regeneration associated genes (RAGs) mRNA. Cre recombinase expressed under the Advillin promoter was used for ATF3-exon3 excision in a broad and specific manner in the DRG. Sciatic nerve injury was carried on on mice with a conditional knockout of ATF3 in sensory neurons and ATF3-wt mice and total RNAseq was carried on RNA extracred from on sciatic innervating DRGs (L4-L6) from the injured side ("Inj") and non-injured side (naive / "Na").

2025-05-16 | GSE279906 | GEO

Sciatic nerve crush regulation of ribosome-associated RNA in DRG neurons

Project description:Nerve injury alters transcription and translational processes in cell-type specific manner.Here we probe the effect of sciatic nerve injury on ribosome associated RNA specifically in sensory neurons.Mice were subjected to crush of the sciatic nerve in one side, while the other nerve was spared and used as naive control condition.

2025-05-16 | GSE230722 | GEO

RNA-seq analysis about Lx8-SINE B2 knocked down samples

Project description:We identified a novel long non-coding RNA Lx8-SINE B2, that is a marker of pluripotency. Depletion of Lx8-SINE B2 impacts embryonic stem cell self-renewal. RNA-seq analysis of Lx8-SINE B2 depletion revealed that a number of glycolytic genes with decreased expression. Mechanistically, we found that the Lx8-SINE B2 activates the glycolysis pathway by binding to Eno1. Collectively, our data suggest that Lx8-SINE B2 maintains the self-renewal of mESCs through glycolysis.

2022-09-19 | GSE182247 | GEO

Sciatic nerve crush regulation of RNA alternative poly-adenylation [DRGinjury_2019-QuantSeq_Rev_24h]

2025-05-16 | GSE233824 | GEO

DLK-gated responses in motoneurons following sciatic nerve crush

Project description:To profile downstream gene-expression changes regulated by DLK, we profiled motoneurons in the lumbar spinal cord using RiboTag, following sciatic nerve crush in both control and Dlk conditional knockout (Dlk ΔMN) mice. We found that DLK regulates the expression of many secreted proteins, which have the potential to influence the behavior of other cells, including the immune system.

2024-01-22 | GSE213987 | GEO

B2 SINE expression during MHV68 infecton

Project description:Short interspersed nuclear elements (SINEs) are retrotransposons evolutionarily derived from endogenous RNA Polymerase III RNAs. Though SINE elements have undergone exaptation into gene regulatory elements, how transcribed SINE RNA impacts transcriptional and post-transcriptional regulation is largely unknown. This is partly due to a lack of information regarding which of the loci have transcriptional potential. Here, we present an approach (short interspersed nuclear element sequencing, SINE-seq), which selectively profiles RNA Polymerase III-derived SINE RNA, thereby identifying transcriptionally active SINE loci. Applying SINE-seq to monitor murine B2 SINE expression during a gammaherpesvirus infection revealed transcription from 28,270 SINE loci, with ~50% of active SINE elements residing within annotated RNA Polymerase II loci. Furthermore, B2 RNA can form intermolecular RNA-RNA interactions with complementary mRNAs, leading to nuclear retention of the targeted mRNA via a mechanism involving p54nrb. These findings illuminate a pathway for the selective regulation of mRNA export during stress via retrotransposon activation.

2016-10-31 | GSE85518 | 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