GEO DataSets

(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) 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) 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) 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. more...

Organism:

Bos indicus; Bos indicus x Bos taurus

Type:

Expression profiling by high throughput sequencing; Genome variation profiling by high throughput sequencing

Platforms:

GPL21383 GPL20723

5 Samples

Download data: VCF, XLSX

(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) 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; Bos indicus x Bos taurus

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) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array; SNP genotyping by SNP array; Expression profiling by high throughput sequencing

Platforms:

GPL16288 GPL18544

40 Samples

Download data

(Submitter supplied) 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. more...

Organism:

Homo sapiens

Type:

SNP genotyping by SNP array; Genome variation profiling by SNP array

Platform:

GPL18544

30 Samples

Download data: TXT

(Submitter supplied) 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. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16288

10 Samples

Download data: TXT

(Submitter supplied) Using two complementary approaches, analysis of imprinting of candidate genes by pyrosequencing and expression profiling of parthenogenetic fetuses, we carried a comprehensive survey of genomic imprinting in swine. In the case of imprinted genes where transcription of one of the two parental alleles is silenced, uniparental embryos like parthenotes can be used to measure transcript dosage effects. Using Affymetrix Porcine GeneChip microarrays, four tissues of day 30 fetuses were profiled: brain, fibroblast, liver, and placenta. more...

Organism:

Sus scrofa

Type:

Expression profiling by array

Platform:

GPL6472

24 Samples

Download data: CEL

(Submitter supplied) The human genome encodes hundreds of tRNA genes but their individual contribution to the tRNA pool is not fully understood. Deep sequencing of tRNA transcripts (tRNA-Seq) can estimate tRNA abundance at single gene resolution, but tRNA structures and post-transcriptional modifications impair these analyses. Here we present a bioinformatics strategy to investigate differential tRNA gene expression and use it to compare tRNA-Seq datasets from cultured human cells and human brain. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL11154

8 Samples

Download data: XLS

(Submitter supplied) These data represent the ratios of charged to total tRNA for E. coli auxotrophic strain CP78 during starvation for leucine over a time course of 32 minutes. Keywords: time-course

Organism:

Bacillus subtilis; Escherichia coli; Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL1746

5 Samples

Download data

(Submitter supplied) We conducted a genome-wide survey of genes in Ae. aegypti females that are transcriptionally responsive upon challenge with dengue virus (serotype-2). The array was designed with 60-mer oligos specific to 16,092 gene transcripts of gene build AaegL1.1 (www. vectorbase.org). The hybridizations were performed at NimbleGen. We provided total RNA purified from the infected and control samples to NimbleGen. more...

Organism:

Aedes aegypti

Type:

Expression profiling by array

Platform:

GPL8705

15 Samples

Download data: PAIR

(Submitter supplied) The number of tRNA isodecoders has increased dramatically in mammals, but the specific molecular and physiological reasons for this expansion remain elusive. To address this fundamental question we used CRISPR editing to knockout the seven-membered phenylalanine tRNA gene family in mice, both individually and combinatorially. Using ATAC-Seq, RNA-seq and proteomics we observed distinct molecular consequences of individual tRNA deletions. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

24 Samples

Download data: TXT