Filters
Technology
Platform
SRP060389
Sus scrofa
7 Downloadable Samples
Illumina Genome Analyzer II
Description
The ability to mature oocytes in vitro provides a tool for creating embryos by parthenogenesis, fertilization and cloning. Unfortunately the quality of oocytes matured in vitro falls behind that of in vivo matured oocytes. To address this difference transcriptional profiling by deep sequencing was conducted on pig oocytes that were either matured in vitro or in vivo. Alignment of over 18 million reads identified 1,316 transcripts that were differentially represented. One pathway that was overrepresented in the oocytes matured in vitro was for Wingless-type MMTV integration site (WNT) signaling. In an attempt to inhibit the WNT pathway Dickkopf-related protein 1 was added to the in vitro maturation medium. Addition of Dickkopf-related protein 1 improved the percentage of oocytes that matured to the metaphase II stage, increased the number of nuclei in the resulting blastocyst stage embryos, and in oocytes reduced the amount of disheveled segment polarity protein 1 protein. It is concluded that transcriptional profiling is a powerful method for detecting differences between in vitro and in vivo matured oocytes, and that the WNT signaling pathway is important for proper oocyte maturation.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part, Disease, Disease stage, Cell line, Treatment
View Samples- Ovis aries
- 10 Downloadable Samples
Ovine Gene 1.1 ST Array (ovigene11st)
Description
Objectives were to determine the effect of supplying butyrate post-ruminally on gene expression in the duodenum of growing polled Dorset lambs.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part
View Samples- Gallus gallus
- 45 Downloadable Samples
- Illumina HiSeq 2500
Description
The main objective of this study was to decipher the gene expression profile associated with the onset and early development of Wooden Breast Disease in commercial broiler chickens. To achieve this, pectoralis major muscle biopsy samples were harvested from high-breast-muscle-yield, purebred broiler line. The pectoral biopsy samples were collected from the cranial (week 2 and 3) and caudal (week 4) aspects of the muscle belly in birds which were allowed to grow up to 7 weeks of age. Three subsets of biopsy samples comprising 6 unaffected (U) and 10 affected (A) from week 2 and 4 and 4U and 12A from week 3 were processed for RNA-sequencing analysis. All selected samples were processed using Truseq stranded mRNA LT sample kit for paired-end 2x75-nucleotide sequencing with Illumina Hiseq 2500 sequencer.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part, Disease
View Samples- Gallus gallus
- 33 Downloadable Samples
- Illumina HiSeq 2500
Description
No description.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part, Cell line, Treatment
View Samples- Homo sapiens
- 4 Downloadable Samples
- Illumina HiSeq 2500
Description
RNA-Seq analysis of intestinal integrity-relevant genes in Caco-2 cell line exposure to aflatoxins M1 and ochratoxin A
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part, Disease, Cell line, Race
View Samples- Ovis aries
- 40 Downloadable Samples
- Affymetrix Bovine Genome Array (bovine)
Description
Expression profiling of sheep born to Australian industry sires with high and low genetic merit (Estimated Breeding Values or EBVs) for eye muscle depth (EMD). Progeny (40) from six Poll Dorset sires representing well defined extremes of EBVs for Eye Muscle Depth (low EBV EMD and high EBV EMD) were selected for analysis. The six sires were Australian industry sires with three sires representative of low EBV EMD and three representing high EBV EMD.
Publication Title
An Always Correlated gene expression landscape for ovine skeletal muscle, lessons learnt from comparison with an "equivalent" bovine landscape.
Sample Metadata Fields
No sample metadata fields
View Samples- Ovis aries
- 15 Downloadable Samples
- Affymetrix Bovine Genome Array (bovine)
Description
Expression data from Sheep longissimus dorsi (LD) muscle during development; fetal lambs (80, 100, 120 days gestation), new born lambs at birth (150 d) and lambs at 12 weeks (230 d)
Publication Title
A gene network switch enhances the oxidative capacity of ovine skeletal muscle during late fetal development.
Sample Metadata Fields
No sample metadata fields
View Samples- Ovis aries
- 8 Downloadable Samples
- Affymetrix Bovine Genome Array (bovine)
Description
The ovine Callipyge mutation causes postnatal muscle hypertrophy localized to the pelvic limbs and torso, as well as body leanness. The mechanism underpinning enhanced muscle mass is unclear, as is the systemic impact of the mutation. Using muscle fibre typing immunohistochemistry we confirmed muscle specific effects and demonstrated that affected muscles had greater prevalence and hypertrophy of type 2X fast twitch glycolytic fibres and decreased representation of types 1, 2C, 2A and/or 2AX fibres. To investigate potential systemic effects of the mutation, proton NMR spectra of plasma taken from lambs at 8 and 12 weeks of age were measured. Multivariate statistical analysis of plasma metabolite profiles demonstrated effects of development and genotype but not gender. Plasma from Callipyge lambs at 12 weeks of age, but not 8 weeks, was characterized by a metabolic profile consistent with contributions from the affected hypertrophic fast twitch glycolytic muscle fibres. Microarray analysis of the perirenal adipose tissue depot did not reveal a transcriptional effect of the mutation in this tissue. We conclude that there is an indirect systemic effect of the Callipyge mutation in skeletal muscle in the form of changes of blood metabolites, which may contribute to secondary phenotypes such as body leanness.
Publication Title
Impacts of the Callipyge mutation on ovine plasma metabolites and muscle fibre type.
Sample Metadata Fields
Specimen part
View Samples- Pantholops hodgsonii, Bos taurus, Procapra przewalskii
- 13 Downloadable Samples
- Affymetrix Bovine Genome Array (bovine)
Description
Since the first cloned animal Dolly Sheep was successfully created by using somatic cell nuclear transfer(SCNT) technique. It has become an irreplaceable tool to understand nuclear reprogramming and totipotency and holds huge potentials for regenerative medicine. However, extremely poor development rate of SCNT embryos indicates it is still questionable. The nature of reprogramming oocyte factors and their mechanism of action remain largely unknown.It is evident that the major barrier that hinders the developing iSCNT embryo mainly appears at the time of embryonic genome activation (EGA), which primarily occurs at the eight-cell stage in mammalian. The interspecies somatic cell nuclear transfer (iSCNT) is desired model for nuclear reprogramming research and a powerful tool for discovering the master genome activation genes. In this study, a valuable transcriptome recourse of iSCNT embryos was established, which derived from more than 2000 clone embryos of four different inter-family donor cells. Based on weighted gene co-expression network (WGCNA) approach, we provide an extensive transcriptome analysis of differentially expressed genes(DEG) for iSCNT embryos. The total gene expression patterns of different iSCNT embryos were discussed. 26 cell-specific modules with were identified, and those module significance and GO enriched categories were analyzed. The regulatory pathways of reprogramming barriers were further enriched. As master genome trigger genes, the transcripts related to TFIID subunit, RNA polymerase and Mediator were incomplete activated in iSCNT embryos. This indicated that pioneer factors, present in the cytoplasm of the oocyte, were failed to bind the sequence target on the heterology nuclear genome. This genomic incompatibility between the nuclear donor cell and the cytoplast may be as a major contributing factor causes the developmental failure of iSCNT cloned embryos.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 193 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
PAPER 1:"Identification of novel subgroups of high-risk pediatric precursor B acute lymphoblastic leukemia (B-ALL) by unsupervised microarray analysis: clinical correlates and therapeutic implications. A Children's Oncology Group (COG) study."
Publication Title
Gene expression classifiers for relapse-free survival and minimal residual disease improve risk classification and outcome prediction in pediatric B-precursor acute lymphoblastic leukemia.
Sample Metadata Fields
Sex, Specimen part, Race
View Samples