GEO DataSets

(Submitter supplied) The use of assisted reproductive technologies (ART) can induce a congenital overgrowth condition in humans and ruminants, namely Beckwith-Wiedemann syndrome (BWS) and large offspring syndrome (LOS), respectively. Shared phenotypes and epigenotypes have been found between BWS and LOS. We have observed global misregulation of transcripts in bovine foetuses with LOS. microRNAs (miRNAs) are important post-transcriptional gene expression regulators. more...

Organism:

Bos indicus x Bos taurus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL25325

45 Samples

Download data: TXT

(Submitter supplied) Embryos generated with the use of assisted reproductive technologies (ART) can develop overgrowth syndromes. In ruminants, the condition is referred to as large offspring syndrome (LOS) and exhibits variable phenotypic abnormalities including overgrowth, enlarged tongue, and abdominal wall defects. These characteristics recapitulate those observed in the human loss-of-imprinting (LOI) overgrowth syndrome Beckwith-Wiedemann (BWS). more...

Organism:

Bos indicus x Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21383

32 Samples

Download data: TXT

(Submitter supplied) Assisted reproductive therapies (ART) have become increasingly common worldwide and up to ~6% of children currently born in developed countries were conceived employing these technologies. Numerous retrospective studies have suggested that ART-conceived children are more likely to develop the overgrowth syndrome Beckwith-Wiedemann (BWS). In bovine, the use of ART can induce a similar overgrown condition, which is referred to as large offspring syndrome (LOS). more...

Organism:

Bos indicus x Bos taurus

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL22943 GPL22942

8 Samples

Download data: BW

(Submitter supplied) Large/abnormal offspring syndrome (LOS/AOS) is a congenital overgrowth syndrome reported in ruminants produced by assisted reproduction (ART-LOS) which exhibit global disruption of the epigenome and transcriptome. LOS/AOS shares phenotypes and epigenotypes with the human congenital overgrowth condition Beckwith-Wiedemann syndrome. We have reported that LOS occurs spontaneously (SLOS), however, to date, no study has been conducted to determine if SLOS has the same methylome epimutations as ART-LOS. more...

Organism:

Bos taurus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL24230

38 Samples

Download data: BEDGRAPH

(Submitter supplied) We report the histone retention loci alteration in human sperm cell genome after density selection

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

6 Samples

Download data: TXT

(Submitter supplied) Selected human sperms with ART technique demonstrate many changes in the genetic and epigenetic aspects. There are many evidances shown that DNA damange and histone retention ratio have significant improved after selection with different methods. These changes may relate with DNA epigenetic changes, however no evidance demonstate these relevance. In this study, MeDIP-ChIP method has been employed to detect DNA methylation loci in human sperm genome processed with density selection. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL16353

6 Samples

Download data: GFF, PAIR

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Bos indicus x Bos taurus; Bos indicus

Type:

Other; Genome variation profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platforms:

GPL31971 GPL31972 GPL31970

50 Samples

Download data: BEDGRAPH, VCF

(Submitter supplied) Large offspring syndrome (LOS) and Beckwith-Wiedemann syndrome are a similar epigenetic congenital overgrowth conditions in ruminants and humans, respectively. We have reported global loss-of-imprinting, methylome epimutations, and global misregulation of genes in LOS. However, less than 4% of gene misregulation can be explained with short range (<20Kb) alterations in DNA methylation. Therefore, we hypothesized that methylome epimutations in LOS affect chromosome architecture which results in misregulation of genes located at distances >20Kb in cis and also in trans (other chromosomes). more...

Organism:

Bos indicus x Bos taurus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL31972

8 Samples

Download data: BEDGRAPH

(Submitter supplied) Large offspring syndrome (LOS) and Beckwith-Wiedemann syndrome are a similar epigenetic congenital overgrowth conditions in ruminants and humans, respectively. We have reported global loss-of-imprinting, methylome epimutations, and global misregulation of genes in LOS. However, less than 4% of gene misregulation can be explained with short range (<20Kb) alterations in DNA methylation. Therefore, we hypothesized that methylome epimutations in LOS affect chromosome architecture which results in misregulation of genes located at distances >20Kb in cis and also in trans (other chromosomes). more...

Organism:

Bos indicus

Type:

Genome variation profiling by high throughput sequencing

Platform:

GPL31971

1 Sample

Download data: VCF

(Submitter supplied) Large offspring syndrome (LOS) and Beckwith-Wiedemann syndrome are a similar epigenetic congenital overgrowth conditions in ruminants and humans, respectively. We have reported global loss-of-imprinting, methylome epimutations, and global misregulation of genes in LOS. However, less than 4% of gene misregulation can be explained with short range (<20Kb) alterations in DNA methylation. Therefore, we hypothesized that methylome epimutations in LOS affect chromosome architecture which results in misregulation of genes located at distances >20Kb in cis and also in trans (other chromosomes). more...

Organism:

Bos indicus x Bos taurus

Type:

Other

Platform:

GPL31970

41 Samples

Download data: BEDGRAPH

(Submitter supplied) Background: As couples struggle with infertility and livestock producers wish to rapidly improve genetic merit in their herd, assisted reproductive technologies (ART) have become increasingly popular in human medicine as well as the livestock industry. Utilizing ART can cause an increased risk of congenital overgrowth syndromes, such as Large Offspring Syndrome (LOS) in ruminants. A dysregulation of transcripts has been observed in bovine fetuses with LOS, which is suggested to be a cause of the phenotype. more...

Organism:

Bos indicus x Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32674

17 Samples

Download data: TXT

(Submitter supplied) Our previous study demonstrated a significant upregulation of a large set of miRNAs at the genomic imprinted Dlk1-Dio3 locus in lymphocytes of diverse murine lupus-prone strains. The upregulation of Dlk1-Dio3 miRNAs in lupus-prone mice is correlated with the global DNA hypomethylation. In this study, by performing genome-wide DNA methylation analysis, we reported that Dlk1-Dio3 genomic region in CD4+ T cells of MRL/lpr mice was hypomethylated, further linking hypomethylation to the increased expression of Dlk1-Dio3 miRNAs in lupus. more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL24247 GPL21103

10 Samples

Download data: XLSX

(Submitter supplied) We established three new rhesus embryonic stem cells lines and conducted their microRNA profilings by Solexa sequencing. Sequencing of small RNA libraries yielded 12.66 million, 13.12 million and 11.57 million raw reads from IVF1.2, IVF3.2 and IVF3.3, respectively. After filtering, we obtained 10.89 million (IVF1.2), 10.60 million (IVF3.2) and 9.26 million (IVF3.3) clean reads (18-30nt).

Organism:

Macaca mulatta

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13267

3 Samples

Download data

(Submitter supplied) MicroRNA and other types of small regulatory RNAs play a crucial role in the regulation of gene expression in eukaryotes. Several distinct classes of small regulatory RNAs have been discovered in recent years. To extend the repertoire of small regulatory RNAs characterized in mammals and identify miRNA expressed upon viral infection we used Illumina’s ultrahigh throughput sequencing approach. Results presented in this study extend our knowledge of the biology and evolution of small regulatory RNAs in mammals and illuminate mechanisms of small RNA biogenesis and function. more...

Organism:

Bos taurus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9323

3 Samples

Download data: FA

(Submitter supplied) The callipyge phenotype is a monogenic muscular hypertrophy that is only expressed in heterozygous sheep receiving the CLPG mutation from their sire. The wild-type phenotype of CLPG/CLPG animals is thought to result from translational inhibition of paternally expressed DLK1 transcripts by maternally expressed miRNAs. To identify the miRNA responsible for this trans-effect, we used high-throughput sequencing to exhaustively catalogue miRNAs expressed in skeletal muscle of sheep of the four CLPG genotypes. more...

Organism:

human gammaherpesvirus 4; Human gammaherpesvirus 8; Betapolyomavirus macacae; Ovis aries; Rattus norvegicus; JC polyomavirus; Human immunodeficiency virus 1; Mus musculus; Human alphaherpesvirus 1; Homo sapiens; Human betaherpesvirus 5; Betapolyomavirus hominis

Type:

Non-coding RNA profiling by array

Platform:

GPL7724

8 Samples

Download data: TXT

(Submitter supplied) Assisted reproductive technology (ART) is an important part of reproductive medicine that comprises superovulation, in vitro fertilization (IVF), in vitro culture of embryos, cryopreservation and embryo transfer. Because it occurs in the sensitive period of gametogenesis and early embryonic development, its possible health effects on the offspring have received widespread attention in recent years. Relevant studies, though, are limited to postnatal follow-up and blood sample analysis. In this study, a mouse model was used to explore the effect of ART on gene expression in the organs of the off-spring using next-generation sequencing. The results showed that it caused abnormal expression in 1060 and 179 genes in the heart and spleen, respectively. Differentially expressed genes (DEGs) in the heart are mainly enriched in RNA synthesis and processing, and cardiovascular system development is also enriched. STRING analysis identified Ccl2, Ptgs2, Rock1, MAPK14, Agt, Wnt5a as core interaction factors. DEGs in the spleen are significantly enriched in anti-infection and im-mune responses and in the hematopoiesis-related pathway "hematopoietic cell lineage", which includes the core factors Fos, Jun and Il1r2. Then, we explored the effects of ART on epigenetic modifiers and imprinted genes. The results showed that 42 heart genes and 5 spleen genes were abnormally expressed, most of which were related to histone modification and chromatin remodeling. Imprinted genes are very important for normal fetal and individual growth and development. It was found that the expression of imprinted genes Dhcr7, Igf2, Mest and Smoc1 decreased in the heart of ART offspring, and the DNA methylation levels of Igf2 and Mest imprinting control regions (ICRs) increased abnormally. Therefore, we con-cluded that, in the mouse model, ART can interfere with the gene expression pattern in the heart and spleen of the adult offspring, causing potentially adverse effects on organ function. The results of this study can provide a reference for evaluating the safety of human ART and helping improve the clinical system.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

11 Samples

Download data: TXT