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LncReader: identification of dual functional long non-coding RNAs using multi-head self-attention mechanism [Ribo-seq]

ABSTRACT: LncReader: identification of dual functional long non-coding RNAs using multi-head self-attention mechanism [Ribo-seq]

PROVIDER: PRJNA831863 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18915702_1.fastq.gz	Fastqsanger.gz
	SRR18915702_2.fastq.gz	Fastqsanger.gz
	SRR18915703_1.fastq.gz	Fastqsanger.gz
	SRR18915703_2.fastq.gz	Fastqsanger.gz
	SRR18915704_1.fastq.gz	Fastqsanger.gz

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LncReader: identification of dual functional long non-coding RNAs using multi-head self-attention mechanism [Ribo-seq]

Project description:The dual functional lncRNAs have been intensively studied and identified to be involved in various fundamental cellular processes recently. It is essential to understand in which context when a dual functional lncRNA serves as a non-coding RNA or a template for coding peptide, particularly in some pathological conditions. However, apart from time consuming and cell type specific experiments, there is virtually no in-silico method for predicting the identity of dual functional lncRNAs. Here, we developed a deep-learning model with multi-head self-attention mechanism, LncReader, to identify dual functional lncRNAs based on their sequence, physicochemical and secondary structural features. Our data demonstrated that LncReader showed multiple advantage compared to various classical machine learning methods. Moreover, to obtain independent in-house datasets for robust testing, mass spectrometry proteomics combined with RNA-seq were applied in four leukemia cell lines. Remarkably, LncReader achieved the best performance among all these datasets. Therefore, LncReader provides a sophisticated and practical tool that enables fast dual functional lncRNAs identification.

2022-04-26 | GSE201484 | GEO

LncReader: identification of dual functional long non-coding RNAs using multi-head self-attention mechanism

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LncReader: identification of dual functional long non-coding RNAs using multi-head self-attention mechanism [RNA-seq]

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LncReader: identification of dual functional long non-coding RNAs using multi-head self-attention mechanism

Project description:LncReader: identification of dual functional long non-coding RNAs using multi-head self-attention mechanism

| PRJNA831861 | ENA

LncReader: identification of dual functional long non-coding RNAs using multi-head self-attention mechanism [RNA-seq]

Project description:LncReader: identification of dual functional long non-coding RNAs using multi-head self-attention mechanism [RNA-seq]

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Stress regulation of sustained attention and the cholinergic attention system

Project description:Stress regulation of sustained attention and the cholinergic attention system

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LncReader: identification of dual functional long non-coding RNAs using multi-head self-attention mechanism

Project description:This SuperSeries is composed of the SubSeries listed below.

2022-04-26 | GSE201485 | GEO

Stress regulation of sustained attention and the cholinergic attention system

Project description:Background: Stress exacerbates symptoms of schizophrenia and attention deficit hyperactivity disorder, which are characterized by impairments in sustained attention. Yet how stress regulates attention remains largely unexplored. Here we investigated whether a 6-day variable stressor (VS) altered sustained attention and the cholinergic attention system in male and female rats. Methods: Sustained attention was tested with the sustained attention task (SAT). Successful performance on SAT relies on the release of acetylcholine (ACh) into the cortex from cholinergic neurons in the nucleus basalis of Meynert (NBM). Thus, we evaluated whether VS altered the morphology of these neurons with a novel approach using Cre-dependent virus in genetically modified ChAT::Cre rats, a species used for this manipulation only. Next, electrochemical recordings measured cortical ACh following VS. Finally, we used RNAseq to identify VS-induced transcriptional changes in the NBM. Results: VS impaired attentional performance in SAT and increased the dendritic complexity of NBM cholinergic neurons in both sexes. NBM cholinergic neurons are mainly under inhibitory control, so this morphological change could increase inhibition on these neurons, reducing downstream ACh release to impair attention. Indeed, VS decreased ACh release in the prefrontal cortex of males. Quantification of global transcriptional changes revealed that, although VS induced many sex-specific changes in gene expression, it increased several signaling molecules in both sexes.

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HNSCC samples vs. normal tonsil samples: self-self hybridization design

Project description:transcription profiling of human head and neck squamous cell carcinoma (HNSCC) samples vs. normal tonsil samples using a self-self hybridization experimental design on two-color arrays. Used to identify differentially expressed genes in tumor/normal samples, and compare the result to that of the same samples using the reference design experimental setting. Keywords: tumor/normal comparison 8 HNSCC tumor samples and 8 normal tonsil samples. Each was profiled using a self-self hybridization design, where two aliquots of the same sample were labeled with two different dyes (cy3 and cy5) and hybridize to the same array.

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