Ontology highlight
ABSTRACT:
PROVIDER: PRJNA244578 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1220300_1.fastq.gz | Fastqsanger.gz | |||
| SRR1220300_2.fastq.gz | Fastqsanger.gz | |||
| SRR1220310_1.fastq.gz | Fastqsanger.gz | |||
| SRR1220310_2.fastq.gz | Fastqsanger.gz | |||
| SRR1220320_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Using RNA sequencing for identifying gene imprinting and random monoallelic expression in human placenta (RNA-seq)
| PRJNA243888 | ENA
Project description:Using RNA sequencing for identifying gene imprinting and random monoallelic expression in human placenta (SNP genotyping)
| PRJNA244577 | ENA
Project description:Given the possible critical importance of placental gene imprinting and random monoallelic expression on fetal and infant health, most of those genes must be identified, in order to understand the risks that the baby might meet during pregnancy and after birth. Therefore, the aim of the current study was to introduce a workflow and tools for analyzing imprinted and random monoallelic gene expression in human placenta, by applying whole-transcriptome (WT) RNA sequencing of placental tissue and genotyping of coding DNA variants in family trios. Ten family trios, each with a healthy spontaneous single-term pregnancy, were recruited. Total RNA was extracted for WT analysis, providing the full sequence information for the placental transcriptome. Parental and child blood DNA genotypes were analyzed by exome SNP genotyping microarrays, mapping the inheritance and estimating the abundance of parental expressed alleles. Imprinted genes showed consistent expression from either parental allele, as demonstrated by the SNP content of sequenced transcripts, while monoallelically expressed genes had random activity of parental alleles. We revealed 4 novel possible imprinted genes (LGALS8, LGALS14, PAPPA2 and SPTLC3) and confirmed the imprinting of 4 genes (AIM1, PEG10, RHOBTB3 and ZFAT-AS1) in human placenta. The major finding was the identification of 4 genes (ABP1, BCLAF1, IFI30 and ZFAT) with random allelic bias, expressing one of the parental alleles preferentially. The main functions of the imprinted and monoallelically expressed genes included: i) mediating cellular apoptosis and tissue development; ii) regulating inflammation and immune system; iii) facilitating metabolic processes; and iv) regulating cell cycle. Placentas from ten family trios were analysed using RNA-Seq.
2014-09-01 | E-GEOD-56524 | biostudies-arrayexpress
Project description:Given the possible critical importance of placental gene imprinting and random monoallelic expression on fetal and infant health, most of those genes must be identified, in order to understand the risks that the baby might meet during pregnancy and after birth. Therefore, the aim of the current study was to introduce a workflow and tools for analyzing imprinted and random monoallelic gene expression in human placenta, by applying whole-transcriptome (WT) RNA sequencing of placental tissue and genotyping of coding DNA variants in family trios. Ten family trios, each with a healthy spontaneous single-term pregnancy, were recruited. Total RNA was extracted for WT analysis, providing the full sequence information for the placental transcriptome. Parental and child blood DNA genotypes were analyzed by exome SNP genotyping microarrays, mapping the inheritance and estimating the abundance of parental expressed alleles. Imprinted genes showed consistent expression from either parental allele, as demonstrated by the SNP content of sequenced transcripts, while monoallelically expressed genes had random activity of parental alleles. We revealed 4 novel possible imprinted genes (LGALS8, LGALS14, PAPPA2 and SPTLC3) and confirmed the imprinting of 4 genes (AIM1, PEG10, RHOBTB3 and ZFAT-AS1) in human placenta. The major finding was the identification of 4 genes (ABP1, BCLAF1, IFI30 and ZFAT) with random allelic bias, expressing one of the parental alleles preferentially. The main functions of the imprinted and monoallelically expressed genes included: i) mediating cellular apoptosis and tissue development; ii) regulating inflammation and immune system; iii) facilitating metabolic processes; and iv) regulating cell cycle.
2014-09-01 | GSE56524 | GEO
Project description:Given the possible critical importance of placental gene imprinting and random monoallelic expression on fetal and infant health, most of those genes must be identified, in order to understand the risks that the baby might meet during pregnancy and after birth. Therefore, the aim of the current study was to introduce a workflow and tools for analyzing imprinted and random monoallelic gene expression in human placenta, by applying whole-transcriptome (WT) RNA sequencing of placental tissue and genotyping of coding DNA variants in family trios. Ten family trios, each with a healthy spontaneous single-term pregnancy, were recruited. Total RNA was extracted for WT analysis, providing the full sequence information for the placental transcriptome. Parental and child blood DNA genotypes were analyzed by exome SNP genotyping microarrays, mapping the inheritance and estimating the abundance of parental expressed alleles. Imprinted genes showed consistent expression from either parental allele, as demonstrated by the SNP content of sequenced transcripts, while monoallelically expressed genes had random activity of parental alleles. We revealed 4 novel possible imprinted genes (LGALS8, LGALS14, PAPPA2 and SPTLC3) and confirmed the imprinting of 4 genes (AIM1, PEG10, RHOBTB3 and ZFAT-AS1) in human placenta. The major finding was the identification of 4 genes (ABP1, BCLAF1, IFI30 and ZFAT) with random allelic bias, expressing one of the parental alleles preferentially. The main functions of the imprinted and monoallelically expressed genes included: i) mediating cellular apoptosis and tissue development; ii) regulating inflammation and immune system; iii) facilitating metabolic processes; and iv) regulating cell cycle.
2014-09-01 | GSE56685 | GEO
Project description:Genomic imprinting is an epigenetic mechanism that leads to parental-allele-specific gene expression. Approximately 150 imprinted genes have been identified in humans and mice but less than 30 genes have been described as imprinted in cattle. For the purpose of de novo identification of imprinted genes in bovine, we determined global monoallelic gene expression in brain, skeletal muscle, liver, kidney and placenta of day ~105 Bos taurus indicus X Bos taurus taurus F1 conceptuses using RNA sequencing. For this, we developed a bioinformatics pipeline to identify parental-specific SNPs after filtering A-to-I RNA editing sites. We identified 53 genes subject to monoallelic expression. A total of 23 are genes known to be imprinted in the cow and 7 are previously-characterized imprinted genes in human and/or mouse that have not be reported to be imprinted in cattle. Of the remaining 23 genes, we found that 10 are uncharacterized or unannotated transcripts located in known imprinting clusters, whereas the other 13 genes are distributed across the bovine genome and not close to any known imprinting clusters. To exclude potential cis-eQTL effects on allelic expression, we corroborated the parental specificity of monoallelic expression in day 86 Bos taurus taurus X Bos taurus taurus F1s and identified eight novel imprinted genes in bovine. Further, we identified 671 candidate A-to-I RNA editing sites and describe imprinted X inactivation in the bovine trophectoderm-derived CT1 cell line. Our results expand the imprinted gene list in bovine and demonstrate that monoallelic gene expression can be the result of cis-eQTL effect.
2016-08-17 | GSE77389 | GEO
Project description:Random monoallelic expression is defined by the allele-specific expression of genes, and by the fact that for an individual cell this monoallelic expression is neither obligate nor necessarily coordinated with the allelic expression in other cells. In order to find novel examples of random monoallelic expression in mouse, we did a transcriptome-wide survey of allele-specific gene expression in two different immortalized cell types. Lymphoblast cell lines and fibroblast cell lines were established (both clonal and nonclonal) and were used as a source of both nuclear RNA and genomic DNA. These samples were assessed for allele-specific gene expression using a custom-designed Mouse SNP Chip. A large number of genes (over 10% of those that were assessed in lymphoblast clones) displayed random monoallelic expression.
2012-02-10 | GSE35678 | GEO
Project description:Fetal health is dependent upon the epigenetic-based regulation of gene expression in placenta. Genomic imprinting is an epigenetic phenomenon common to placenta and refers to the monoallelic expression of a gene in a parental-specific manner. We aimed to detect novel imprinted genes in human placenta by applying whole transcriptome RNA-sequencing and genotyping of coding variants. Ten family trios with healthy spontaneous single term pregnancy were recruited. Parental and child DNA genotypes were analysed using exome SNP genotyping microarrays, revealing the inheritance of parental alleles. Total RNA was extracted from placental tissue for whole transcriptome analysis. The imprinted genes showed consistent expression from either parental allele as demonstrated by the SNP content of sequenced transcripts. We found seven novel imprinted genes (ABP1, BCLAF1, IFI30, LGALS8, LGALS14, PAPPA2 and SPTLC3) and confirmed five known imprinted genes (AIM1, PEG10, RHOBTB3, ZFAT and ZFAT-AS1). The main functions of the proteins encoded by the imprinted genes can be grouped as being involved in: i) cellular apoptosis and tissue development; ii) regulating inflammation and modulating the immune system; iii) facilitating metabolic processes and iv) regulating the cell cycle. Ten family trios (mother, father, child) were analysed using SNP genotyping. Raw data contains additional two samples that were not used.
2014-09-01 | E-GEOD-56685 | biostudies-arrayexpress
Project description:The maternal and paternal copies of the genome are both required for mammalian development and this is primarily due to imprinted genes, those that are mono-allelically expressed based on parent-of-origin. Typically, this pattern of expression is regulated by differentially methylated regions (DMRs) that are established in the germline and maintained after fertilisation. There are a large number of germline DMRs that have not yet been associated with imprinting and their function in development is unknown. In this study, we developed a genome-wide approach to identify novel imprinted DMRs, specifically in the human placenta, and investigated the dynamics of imprinted DMRs during development in somatic and extra-embryonic tissues. DNA methylation was evaluated using the Illumina HumanMethylation450 array in 116 human tissue samples, publically available reduced representation bisulfite sequencing in the human embryo and germ cells, and targeted bisulfite sequencing in term placentas. 43 known and 101 novel imprinted DMRs were identified in the human placenta, by comparing methylation between diandric and digynic triploids and female and male gametes. 72 novel DMRs showed a pattern consistent with placental-specific imprinting and this monoallelic methylation was entirely maternal in origin. Strikingly, these DMRs exhibited polymorphic imprinted methylation specifically in placenta. These data suggest that imprinting in human development is far more extensive and dynamic than previously reported and that the placenta preferentially maintains maternal germline-derived DNA methylation.
2015-12-23 | GSE76273 | GEO
Project description:Parental imprinting results in a monoallelic parent-of-origin dependent gene expression. However, many imprinted genes identified by differential methylation do not exhibit complete monoallelic expression. Previous studies demonstrated a complex tissue-dependent expression patterns for some imprinted genes. Still, the complete magnitude of this phenomenon remains largely unknown. Differentiating human parthenogenetic induced pluripotent stem cells into different cell types and combining DNA methylation with novel 5' RNA sequencing methodology, enabled us to identify tissue- and isoform-dependent imprinted genes in a genome wide manner. We show that nearly half of all imprinted genes expresses both biallelic and monoallelic isoforms, that are controlled by tissue specific alternative promoters. This study provides the first global analysis of tissue-specific imprinting in humans, and implies that alternative promoters are central in the regulation of imprinted genes. Gene expression analysis was performed on a total of 6 human cell lines, including 4 iPSCs differentiated to neural progenitors and sorted using NCAM1 (2 control and 2 Parthenogenetic), and 2 iPSCs differentiated to endodermal progenitors (1 Control and 1 Parthenogenetic)
2016-07-03 | E-GEOD-65002 | biostudies-arrayexpress