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RNA-sequencing reveals predominance of THRA splicing isoform 2 in developing human brain [treated]

ABSTRACT: RNA-sequencing reveals predominance of THRA splicing isoform 2 in developing human brain [treated]

PROVIDER: PRJNA1052106 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR27202044_1.fastq.gz	Fastqsanger.gz
	SRR27202044_2.fastq.gz	Fastqsanger.gz
	SRR27202045_1.fastq.gz	Fastqsanger.gz
	SRR27202045_2.fastq.gz	Fastqsanger.gz
	SRR27202046_1.fastq.gz	Fastqsanger.gz

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RNA-sequencing reveals predominance of THRA splicing isoform 2 in developing human brain

Project description:RNA-sequencing reveals predominance of THRA splicing isoform 2 in developing human brain

| PRJNA1052096 | ENA

RNA-sequencing reveals predominance of THRA splicing isoform 2 in developing human brain [untreated]

Project description:RNA-sequencing reveals predominance of THRA splicing isoform 2 in developing human brain [untreated]

| PRJNA1052102 | ENA

RNA-sequencing reveals strong predominance of THRA splicing isoform 2 in the developing and adult human brain

Project description:RNA-sequencing reveals strong predominance of THRA splicing isoform 2 in the developing and adult human brain

| PRJNA929982 | ENA

RNA-sequencing reveals strong predominance of THRA splicing isoform 2 in the developing and adult human brain

Project description:Thyroid hormone receptor alpha (THRα) is a nuclear hormone receptor that binds triiodothyronine (T3) and acts as an important transcription factor in development, metabolism and reproduction. THRα has in mammals two major splicing isoforms, THRα1 and THRα2. The better characterized isoform, THRα1, is a transcriptional stimulator of genes involved in cell metabolism and growth. The less well characterized isoform, THRα2, lacks the Ligand Binding Domain (LBD) and is thought to act as an inhibitor of THRα1 action. The ratio of THRα1 to THRα2 splicing isoforms is therefore critical for transcriptional regulation in different tissues and during development. However, the expression patterns of both isoforms have not been studied in healthy human tissues or in the developing brain. Given the lack of commercially available isoform-specific antibodies, we addressed this question by analyzing four bulk RNA-sequencing datasets and two scRNA-sequencing datasets to determine the RNA expression levels of human THRA1 and THRA2 transcripts in healthy adult tissues and in the developing brain. We demonstrate how 10X Chromium scRNA-seq datasets can be used to perform splicing-sensitive analyses of isoforms that differ at the 3'-end. In all datasets, we discovered a strong predominance of THRA2 transcripts at all stages of brain development and in central nervous system from healthy human adults.

2024-09-12 | GSE224153 | GEO

RNA-sequencing reveals predominance of THRA splicing isoform 2 in developing human brain [untreated]

Project description:Thyroid Hormone Receptor α (THRα) is a nuclear hormone receptor for triiodothyronine (T3) that acts as a transcription factor. Depending on its splicing pattern, it may act either as a stimulator or inhibitor of gene transcription. The relative proportions of the THRα splicing isoforms (THRα1 versus THRα2) in different tissues are crucial for the outcome of transcription regulation. To date, the tissue-specific expression patterns of the two main isoforms in human cortical development have not been determined. To address this gap, we generated cortical brain organoids in vitro following the STEMdiff™ Cerebral Organoid Kit guidelines. We then generated the stranded bulk RNA-Seq dataset here presented. We employed a bioinformatics pipeline to ensure the quality of the dataset and to extract and quantify the read counts specific for our isoforms of interest. We observed a steady increase of THRα transcript in time and a strong predominance of THRα2 transcripts at all stages.

2024-09-12 | GSE250142 | GEO

RNA-sequencing reveals predominance of THRA splicing isoform 2 in developing human brain [treated]

Project description:Thyroid Hormone Receptor α (THRα) is a nuclear hormone receptor for triiodothyronine (T3) that acts as a transcription factor. Depending on its splicing pattern, it may act either as a stimulator or inhibitor of gene transcription. The relative proportions of the THRα splicing isoforms (THRα1 versus THRα2) in different tissues are crucial for the outcome of transcription regulation. To date, the tissue-specific expression patterns of the two main isoforms in human cortical development have not been determined. To address this gap, we generated cortical brain organoids in vitro following the STEMdiff™ Cerebral Organoid Kit guidelines. Samples were treated with 50nM T3 48h before collection to perturb the Thyroid Hormone-regulated system. We then generated the stranded bulk RNA-Seq dataset here presented. We employed a bioinformatics pipeline to ensure the quality of the dataset and to extract and quantify the read counts specific for our isoforms of interest. We observed a steady increase of THRα transcript in time and a strong predominance of THRα2 transcripts at all stages.

2024-09-12 | GSE250143 | GEO

RNA-sequencing reveals predominance of THRA splicing isoform 2 in developing human brain

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

2024-09-12 | GSE250144 | GEO

Cell-Type-Specific Splicing of Transcription Regulators and Ptbp1 by Rbfox1/2/3 in the Developing Neocortex

Project description:This study investigates how master splicing regulators interact and the extent to which transcription regulators are spliced differently during brain development. Cell-type-specific RNA-Seq analyses of the developing neocortex uncover variable expression of the Rbfox1/2/3 genes and enriched splicing events in transcription regulators, altering protein isoforms or inducing nonsense-mediated mRNA decay. Transient expression of Rbfox proteins in radial glial progenitors induces neuronal splicing events preferentially in transcription regulators such as Meis2 and Tead1. Surprisingly, Rbfox proteins promote the inclusion of a mammal-specific alternative exon and a previously undescribed poison exon in Ptbp1. Simultaneous ablation of Rbfox1/2/3 in the neocortex downregulates neuronal isoforms and disrupts radial neuronal migration. Furthermore, the progenitor isoform of Meis2 promotes Tgfb3 transcription, while the Meis2 neuron isoform promotes neuronal differentiation. These observations indicate that transcription regulators are differentially spliced between cell types in the developing neocortex.

2024-12-04 | GSE283469 | GEO

Sam68 regulation of alternative splicing in the developing cerebellum

Project description:We uncover a Sam68-dependent splicing program during cerebellar development. These events direct proper isoform expression of the genes required to guarantee the establishment of the correct spatial/temporal neural circuitry. The dysregulation in Sam68 null mice leads to functional defects in adult neurons

2020-06-01 | GSE133711 | GEO

Next generation sequencing facilitates quantitative analysis of transcriptomes of adult mouse alveolar epithelial type 2 (AT2) cells with Atf3 or Thra overexpression

Project description:Purpose: The goals of this study are to generate transcriptome profiling (RNA-seq) of AT2 cells with over expression of Atf3 and Thra. Methods: AT2 cell mRNA profiles of 5 or 6-week-old wild-type mice were generated by deep sequencing, in triplicate. The Illumina Nextseq 500 system was used to generate raw data at 75 cycles. Fastq files was aligned to the reference genome and DEseq2 was used to analyze the differentially expressed genes. Results: Our results show that Atf3 or Thra overexpression promotes the expression of genes associated AT2 cell proliferation. Conclusions: Our study represents the first detailed analysis of transcriptomes of mouse AT2 cell with Atf3 or Thra overexpression, with biologic replicates, generated by RNA-seq technology.

2022-07-21 | GSE183129 | GEO

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