GEO DataSets

(Submitter supplied) Transcriptomic analysis of 5 IVF-derived bovine blastocysts using Illumina sequencing technology

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15750

5 Samples

Download data: CSV

(Submitter supplied) Background: Mycobacterium bovis, the causative agent of bovine tuberculosis, is an intracellular pathogen that can persist inside host macrophages during infection via a diverse range of mechanisms that subvert the host immune response. In the current study, we have analysed and compared the transcriptomes of M. bovis-infected monocyte-derived macrophages (MDM) purified from six Holstein-Friesian females with the transcriptomes of non-infected control MDM from the same animals over a 24 h period using strand-specific RNA sequencing (RNA-seq). more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15750

14 Samples

Download data: TXT, XLSX

(Submitter supplied) Objective: To study post-hatching development after transfer of morphologically good quality embryos that survived in vitro maturation under lipolytic conditions using a well-established and recognized bovine model. Design: prospective study with a crossover design. Setting: research laboratory. Animals: 8 healthy multiparous non-lactating Holstein cows used in repeated embryo transfers. Intervention(s): Bovine cumulus oocyte complexes (COCs) were in vitro matured in the presence of either 1) a combination of elevated pathophysiological concentration of palmitic acid (PA) and physiological concentrations of stearic acid (SA) and oleic acid (OA) (HIGH PA), or 2) physiological concentrations of PA, SA and OA (BASAL). more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22316

53 Samples

Download data: TXT

(Submitter supplied) Temporal changes in the embryo transcriptome between the blastocyst stage (Day 7) and initiation of elongation (Day 13) differ between in vivo- and in vitro-derived embryos and are reflective of subsequent developmental fate. The aim of this study was to examine the temporal changes in transcriptional profile as the embryo develops from a spherical blastocyst on Day 7 to an ovoid conceptus at the initiation of elongation on Day 13 and to highlight differences in these temporal gene expression dynamics between in vivo- and in vitro-derived blastocysts which may be associated with embryonic survival/mortality using the bovine Affymetrix microarray.

Organism:

Bos taurus

Type:

Expression profiling by array

Platform:

GPL2112

12 Samples

Download data: CEL

(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) Transcriptomes of bovine IVF embryos showing distinct developmental statuses were sequenced

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11153

2 Samples

Download data: TXT

(Submitter supplied) The objective of the current experiment was to identify the transcriptome profile of in vitro-derived embryos with high competence to establish and maintain gestation and in vitro-derived embryos treated with CSF2. Using P < 0.01 and a fold change > 2-fold or < 0.5 fold as cut-offs, there were 617 differentially expressed genes (DEG) between embryos that survived to day 30 vs those that did not, 470 DEG between embryos that survived to day 60 and those that did not, 432 DEG between embryos that maintained pregnancy from day 30 to day 60 vs those where pregnancy failed after day 30, and 635 DEG regulated by CSF2, regardless of pregnancy outcome. more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23055

45 Samples

Download data: TXT

(Submitter supplied) Efforts to improve resilience in livestock production systems have focused on two objectives: investigating the genetic control of immune function as it pertains to robustness and disease resistance, and finding predictive markers for use in breeding programs. In this context, the peripheral blood transcriptome represents an important source of biological information about an individual's health and immunological status, and has been proposed for use as an intermediate phenotype to measure immune capacity. more...

Organism:

Sus scrofa

Type:

Expression profiling by array

Platform:

GPL19893

243 Samples

Download data: TXT

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

Organism:

Bos taurus

Type:

Expression profiling by array; Methylation profiling by genome tiling array

Platforms:

GPL18384 GPL13226

12 Samples

Download data: TXT

(Submitter supplied) Metabolic stress associated with negative energy balance in high producing dairy cattle and obesity in women is a risk factor for decreased fertility. Non-esterified fatty acids (NEFA) are involved in this pathogenesis as they jeopardize oocyte and embryo development. Growing evidence indicates that maternal metabolic disorders can disturb epigenetic programming, and more specifically DNA methylation, in the offspring. more...

Organism:

Bos taurus

Type:

Expression profiling by array

Platform:

GPL13226

4 Samples

Download data: TXT

(Submitter supplied) Metabolic stress associated with negative energy balance in high producing dairy cattle and obesity in women is a risk factor for decreased fertility. Non-esterified fatty acids (NEFA) are involved in this pathogenesis as they jeopardize oocyte and embryo development. Growing evidence indicates that maternal metabolic disorders can disturb epigenetic programming, and more specifically DNA methylation, in the offspring. more...

Organism:

Bos taurus

Type:

Methylation profiling by genome tiling array

Platform:

GPL18384

8 Samples

Download data: TXT

(Submitter supplied) We used RNA sequencing to analyze transcript profiles of ten autopsy brain regions from ten subjects. RNA sequencing techniques were designed to detect both coding and non-coding RNA, splice isoform composition, and allelic expression. Brain regions were selected from five subjects with a documented history of smoking and five non-smokers. Paired-end RNA sequencing was performed on SOLiD instruments to a depth of >40 million reads, using linearly amplified, ribosomally depleted RNA. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome variation profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL20148 GPL16558

98 Samples

Download data: TXT, VCF

(Submitter supplied) Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis. Methods: Retinal mRNA profiles of 21-day-old wild-type (WT) and neural retina leucine zipper knockout (Nrl−/−) mice were generated by deep sequencing, in triplicate, using Illumina GAIIx. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11002

6 Samples

Download data: BAM, TXT, XLS

(Submitter supplied) Sickle cell transcriptome was analyzed using whole blood clinical specimens on the Affymetrix Human Exon 1.0 ST arrays and Illumina’s deep sequencing technologies. Data analysis indicated a strong concordance (R=0.64) between exon array and RNA-seq in both gene level and exon level expression of transcripts. The magnitude of fold changes in the expression levels for the differentially expressed genes (p<0.05) was found to be higher in RNA-seq than microarrays. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5188

10 Samples

Download data: CEL

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

Organism:

Sus scrofa; Bos taurus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL26012 GPL26351

36 Samples

Download data

(Submitter supplied) Compared to other mammalian species, porcine oocytes and embryos are characterized by large amounts of lipids stored mainly in the form of droplets in the cytoplasm. The amount and the morphology of LD change throughout the preimplantation development however, relatively little is known about expression of genes involved in lipid metabolism of early embryos. We compared porcine and bovine blastocyst stage embryos as well as dissected inner cell mass (ICM) and trophoblast (TE) cell populations with regard to lipid droplet storage and expression of genes functionally annotated to selected lipid Gene Ontology terms using RNA-seq. more...

Organism:

Sus scrofa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26351

28 Samples

Download data: CSV

(Submitter supplied) Compared to other mammalian species, porcine oocytes and embryos are characterized by large amounts of lipids stored mainly in the form of droplets in the cytoplasm. The amount and the morphology of LD change throughout the preimplantation development however, relatively little is known about expression of genes involved in lipid metabolism of early embryos. We compared porcine and bovine blastocyst stage embryos as well as dissected inner cell mass (ICM) and trophoblast (TE) cell populations with regard to lipid droplet storage and expression of genes functionally annotated to selected lipid Gene Ontology terms using RNA-seq. more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26012

8 Samples

Download data: CSV

(Submitter supplied) There is an inevitable need for combining in vitro and in vivo culture systems during specific developmental time points to facilitate a comprehensive understanding of early embryo development which would yield insights into the molecular pathways controlling early development and to improve our knowledge in regulation of embryonic development. In current study, we aimed to understand the influences of in vitro culture conditions on bovine blastocyst originated in vivo at 2- or 8-cell stagre. more...

Organism:

Bos taurus

Type:

Expression profiling by array

Platform:

GPL13226

12 Samples

Download data: TXT