Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA335907 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR3990362.fastq.gz | Fastqsanger.gz | |||
| SRR3990363.fastq.gz | Fastqsanger.gz | |||
| SRR3990364.fastq.gz | Fastqsanger.gz |
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Project description:Background: Despite of extensive research the genetic component of extremely low birth weight in newborns has remained obscure. Results: The aim of the case study was to identify candidate gene(s) causing extremely low birth weight (ELBW) in newborns and hypotrophy in infants. A four-member family was studied: mother, father and two ELBW-phenotype children. The studies were carried out due to the medical conditions of the second child at birth and post-partum: peculiar phenotype, micro-anomalies, recurrent infections, suspicion of autoimmune hepatitis, multifactorial encephalopathy, and suspicion of metabolic and chromosomal abnormalities. Whole genome single nucleotide polymorphism (SNP) genotyping array was used to investigate genomic rearrangements in both affected children using peripheral blood DNA samples. Whole blood transcriptome was assessed by using RNA sequencing (RNA-seq) in all four family members. RNA-seq identified a single gene – C14orf132 differentially expressed, with the level of the transcript significantly lower in blood samples of children. Copy number variant (CNV) analysis did not reveal any pathogenic CNVs in the region of C14orf132 gene of both affected children. Conclusion: We showed the importance of combining whole genome CNV and transcriptome analysis in identification of the candidate gene(s) in case studies. We propose the C14orf132 (chromosome 14 open reading frame 132) gene expression to be associated with the ELBW-phenotype. C14orf132 gene is a novel long non-coding RNA (lincRNA) with unknown function, which might be associated with the developmental delay through the altered gene expression Background: Despite of extensive research the genetic component of extremely low birth weight in newborns has remained obscure. Results: The aim of the case study was to identify candidate gene(s) causing extremely low birth weight (ELBW) in newborns and hypotrophy in infants. A four-member family was studied: mother, father and two ELBW-phenotype children. The studies were carried out due to the medical conditions of the second child at birth and post-partum: peculiar phenotype, micro-anomalies, recurrent infections, suspicion of autoimmune hepatitis, multifactorial encephalopathy, and suspicion of metabolic and chromosomal abnormalities. Whole genome single nucleotide polymorphism (SNP) genotyping array was used to investigate genomic rearrangements in both affected children using peripheral blood DNA samples. Whole blood transcriptome was assessed by using RNA sequencing (RNA-seq) in all four family members. RNA-seq identified a single gene – C14orf132 differentially expressed, with the level of the transcript significantly lower in blood samples of children. Copy number variant (CNV) analysis did not reveal any pathogenic CNVs in the region of C14orf132 gene of both affected children. Conclusion: We showed the importance of combining whole genome CNV and transcriptome analysis in identification of the candidate gene(s) in case studies. We propose the C14orf132 (chromosome 14 open reading frame 132) gene expression to be associated with the ELBW-phenotype. C14orf132 gene is a novel long non-coding RNA (lincRNA) with unknown function, which might be associated with the developmental delay through the altered gene expression Background: Despite of extensive research the genetic component of extremely low birth weight in newborns has remained obscure. Results: The aim of the case study was to identify candidate gene(s) causing extremely low birth weight (ELBW) in newborns and hypotrophy in infants. A four-member family was studied: mother, father and two ELBW-phenotype children. The studies were carried out due to the medical conditions of the second child at birth and post-partum: peculiar phenotype, micro-anomalies, recurrent infections, suspicion of autoimmune hepatitis, multifactorial encephalopathy, and suspicion of metabolic and chromosomal abnormalities. Whole genome single nucleotide polymorphism (SNP) genotyping array was used to investigate genomic rearrangements in both affected children using peripheral blood DNA samples. Whole blood transcriptome was assessed by using RNA sequencing (RNA-seq) in all four family members. RNA-seq identified a single gene – C14orf132 differentially expressed, with the level of the transcript significantly lower in blood samples of children. Copy number variant (CNV) analysis did not reveal any pathogenic CNVs in the region of C14orf132 gene of both affected children. Conclusion: We showed the importance of combining whole genome CNV and transcriptome analysis in identification of the candidate gene(s) in case studies. We propose the C14orf132 (chromosome 14 open reading frame 132) gene expression to be associated with the ELBW-phenotype. C14orf132 gene is a novel long non-coding RNA (lincRNA) with unknown function, which might be associated with the developmental delay through the altered gene expression. Background: Despite of extensive research the genetic component of extremely low birth weight in newborns has remained obscure. Results: The aim of the case study was to identify candidate gene(s) causing extremely low birth weight (ELBW) in newborns and hypotrophy in infants. A four-member family was studied: mother, father and two ELBW-phenotype children. The studies were carried out due to the medical conditions of the second child at birth and post-partum: peculiar phenotype, micro-anomalies, recurrent infections, suspicion of autoimmune hepatitis, multifactorial encephalopathy, and suspicion of metabolic and chromosomal abnormalities. Whole genome single nucleotide polymorphism (SNP) genotyping array was used to investigate genomic rearrangements in both affected children using peripheral blood DNA samples. Whole blood transcriptome was assessed by using RNA sequencing (RNA-seq) in all four family members. RNA-seq identified a single gene – C14orf132 differentially expressed, with the level of the transcript significantly lower in blood samples of children. Copy number variant (CNV) analysis did not reveal any pathogenic CNVs in the region of C14orf132 gene of both affected children. Conclusion: We showed the importance of combining whole genome CNV and transcriptome analysis in identification of the candidate gene(s) in case studies. We propose the C14orf132 (chromosome 14 open reading frame 132) gene expression to be associated with the ELBW-phenotype. C14orf132 gene is a novel long non-coding RNA (lincRNA) with unknown function, which might be associated with the developmental delay through the altered gene expression.
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Project description:Bronchopulmonary dysplasia (BPD) is a major complication of preterm birth. This study aimed to identify circulating miRNA biomarkers in peripheral blood of preterm infants for early risk prediction of BPD. Peripheral blood was collected from 41 very low birth weight (VLBW) and extremely low birth weight (ELBW) preterm newborns (BPD+: n=20; BPD-: n=21) at days 10-14 of life. Total RNA was profiled using the Affymetrix GeneChip miRNA 4.1 Array (GeneTitan instrument, 96-well plate format). RMA normalization and limma differential expression identified candidate miRNA biomarkers. Four miRNAs (hsa-let-7b-5p, hsa-miR-27a-3p, hsa-let-7c-5p, hsa-miR-182-5p) were significantly upregulated in BPD infants.
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Project description:Bronchopulmonary dysplasia (BPD) is a major complication of preterm birth, with lasting effects on respiratory outcomes in extremely low birth weight (ELBW) and very low birth weight (VLBW) infants. This pilot study aimed to identify non-invasive salivary microRNA biomarkers for early BPD risk stratification in preterm neonates. Saliva samples were collected from 20 preterm infants (BPD+: n=10; BPD-: n=10) at days 10-14 of life. Total RNA including the miRNA fraction was isolated from saliva using the MagMAX mirVana Total RNA Isolation Kit. RNA was profiled using the Affymetrix GeneChip miRNA 4.1 Array (GeneTitan MC instrument, 96-well plate format). RMA normalization and limma differential expression identified three candidate salivary miRNA biomarkers (hsa-let-7b-5p, hsa-miR-4454, hsa-let-7c-5p), all significantly upregulated in BPD infants.
2026-06-29 | GSE336455 | GEO
Project description:Breast milk has shown neurodevelopmental advantages compared to infant formula, especially in IUGR infants, which may relate to the fat source. This study aimed to compare neurodevelopmental outcomes in normal birth weight (NBW) and intrauterine growth restricted (IUGR) piglets fed a formula diet with either a vegetable oil (VEG) or bovine milk fat source (MILK). Results showed that total plasma lipids were increased by feeding the MILK diet. 82% and 11% of lipid species were differentially expressed between dietary groups in plasma and hippocampus, respectively, with slight agreement between the plasma and brain lipidome. The MILK diet was most effective in increasing brain lipid accretion, mainly comprising phospholipids. Absolute regional brain weights, grey and white matter volumes, and behavior and motor function scores were lower in IUGR piglets with no effects of diet. Cognitive function and gene expression profiles were similar for dietary and weight groups, and overall only minor interactive effects between diet and weight were observed. In conclusion, dietary fat source influenced the plasma and to a lesser degree the hippocampal lipidome, but was unable to improve on IUGR induced brain structural and functional impairments.
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