Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE250144 | GEO | 2024/09/12

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

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 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

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 predominance of THRA splicing isoform 2 in developing human brain [treated]

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

| PRJNA1052106 | 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

Alternative splicing in PTBP2 knockout mouse brain

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-12-01 | E-GEOD-51740 | biostudies-arrayexpress

Sequencing Reveals miRNAs Enriched in the Developing Mouse Enteric Nervous System

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

2023-12-26 | GSE250528 | GEO

Deep sequencing analysis of the developing mouse brain reveals a novel microRNA.

Project description:BACKGROUND: MicroRNAs (miRNAs) are small non-coding RNAs that can exert multilevel inhibition/repression at a post-transcriptional or protein synthesis level during disease or development. Characterisation of miRNAs in adult mammalian brains by deep sequencing has been reported previously. However, to date, no small RNA profiling of the developing brain has been undertaken using this method. We have performed deep sequencing and small RNA analysis of a developing (E15.5) mouse brain. RESULTS: We identified the expression of 294 known miRNAs in the E15.5 developing mouse brain, which were mostly represented by let-7 family and other brain-specific miRNAs such as miR-9 and miR-124. We also discovered 4 putative 22-23 nt miRNAs: mm_br_e15_1181, mm_br_e15_279920, mm_br_e15_96719 and mm_br_e15_294354 each with a 70-76 nt predicted pre-miRNA. We validated the 4 putative miRNAs and further characterised one of them, mm_br_e15_1181, throughout embryogenesis. Mm_br_e15_1181 biogenesis was Dicer1-dependent and was expressed in E3.5 blastocysts and E7 whole embryos. Embryo-wide expression patterns were observed at E9.5 and E11.5 followed by a near complete loss of expression by E13.5, with expression restricted to a specialised layer of cells within the developing and early postnatal brain. Mm_br_e15_1181 was upregulated during neurodifferentiation of P19 teratocarcinoma cells. This novel miRNA has been identified as miR-3099. CONCLUSIONS: We have generated and analysed the first deep sequencing dataset of small RNA sequences of the developing mouse brain. The analysis revealed a novel miRNA, miR-3099, with potential regulatory effects on early embryogenesis, and involvement in neuronal cell differentiation/function in the brain during late embryonic and early neonatal development.

| S-EPMC3088569 | biostudies-literature

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