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GSE21383
Sus scrofa
12 Downloadable Samples
Affymetrix Porcine Genome Array (porcine)
Description
Previous results from a genome scan in a F2 Iberian by Meishan intercross showed several chromosome regions associated with litter size traits. In order to identify candidate genes underlying these QTL we have performed an ovary gene expression analysis during pregnancy. F2 sows were ranked by their estimated breeding values for prolificacy, the six sows with higher EBV (HIGH prolificacy) and the six with lower EBV (LOW prolificacy) were selected. Samples were hybridized to Affymetrix porcine expression microarrays. The statistical analysis with a mixed-model approach identified 221 differentially expressed probes, representing 189 genes. These genes were functionally annotated in order to identify the genetic pathways overrepresented. Among the most represented functional groups the first one was immune system response activation against external stimulus. The second group was made up of genes which regulate the maternal homeostasis by complement and coagulation cascades. The last group was involved on lipid and fatty acid enzymes of metabolic processes, which participate in steroidogenesis pathway. In order to identify powerful candidate genes for prolificacy, the second approach of this study was merging microarray data with position information of QTL affecting litter size, previously detected in the same experimental cross. According to this, we have identified 27 differentially expressed genes co-localized with QTL for litter size traits, which fulfill the biological, positional and functional criteria.
Publication Title
Differential gene expression in ovaries of pregnant pigs with high and low prolificacy levels and identification of candidate genes for litter size.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 12 Downloadable Samples
- Illumina HumanHT-12 V4.0 expression beadchip
Description
Here we used microarray expression profiling to characterise global changes in gene expression during stages of proliferation and differentiation of human neural stem cells
Publication Title
Associations of the Intellectual Disability Gene MYT1L with Helix-Loop-Helix Gene Expression, Hippocampus Volume and Hippocampus Activation During Memory Retrieval.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Sus scrofa
- 24 Downloadable Samples
- Affymetrix Porcine Genome Array (porcine)
Description
This study aimed to characterize differences in gene expression in piglets inoculated with porcine circovirus type 2 (PCV2), the essential causative agent of postweaning multisystemic wasting syndrome (PMWS). Comparisons between control and PCV2-inoculated pigs were done at five different time points: 1, 2, 5, 8, and 29 days post-inoculation.
Publication Title
Time course differential gene expression in response to porcine circovirus type 2 subclinical infection.
Sample Metadata Fields
Age, Specimen part
View Samples- Sus scrofa
- 63 Downloadable Samples
- Affymetrix Porcine Genome Array (porcine)
Description
Artificial selection has resulted in animal breeds with extreme phenotypes. As an organism is made up of many different tissues and organs, each with its own genetic programme, it is pertinent to ask what are the relative contributions of breed or sex when assessed across tissues.
Publication Title
Transcriptome architecture across tissues in the pig.
Sample Metadata Fields
Age
View Samples- Homo sapiens
- 35 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Studying the causes and correlates of natural variation in gene expression in healthy populations assumes that individual differences in gene expression can be reliably and stably assessed across time. However, this is yet to be established.
Publication Title
Assessing individual differences in genome-wide gene expression in human whole blood: reliability over four hours and stability over 10 months.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Mus musculus
- 32 Downloadable Samples
- Affymetrix Mouse Genome 430A 2.0 Array (mouse430a2)
Description
The cholecystokinin B (2) receptor knockout (Cckbr KO) protects against allodynia induced by chronic constriction injury (CCI). The mechanism of this phenomenon is unknown, but must involve persistent changes in pain modulation and/or inflammatory pathways. We performed a gene expression study in two brain areas (midbrain and medulla) after surgical induction of CCI in Cckbr KO and wild-type (wt) control mice. The patterns of gene expression differences suggest that the immune system is activated in higher brain structures following CCI in the wt mice. The strongest differences include genes related to the MAPK pathway activation and cytokine production. In Cckbr KO mice this expressional pattern was absent. In addition, we found significant elevation of the Toll-like receptor 4 (Tlr4) in the supraspinal structures of the mice with deleted Cckbr compared to wt control mice. This up-regulation is most likely induced by the deletion of Cckbr. We suggest that there is a functional deficiency in the Tlr4 pathway which disables the development of neuropathic pain in Cckbr KO mice. Indeed, real time PCR analysis detected a CCI-induced upregulation of Tlr4 and Il1b expression in the lumbar region of wt but not Cckbr KO mice. Gene expression profiling indicates that elements of the immune response are not activated in Cckbr KO mice following CCI. Our findings suggest that there may be a role for CCK in the regulation of innate immunity.
Publication Title
Gene expression profiling reveals upregulation of Tlr4 receptors in Cckb receptor deficient mice.
Sample Metadata Fields
No sample metadata fields
View Samples- Danio rerio
- 18 Downloadable Samples
NextSeq 500
Description
Low incubation temperature during early development negatively affects survival and related innate immune processes in zebrafish larvae exposed to lipopolysaccharide Overall design: Zebrafish embryos were collected from 28 °C, and divided into three temperature groups (24 °C, 28 °C, 32 °C) for incubation. At the first-feeding stage, larvae from each incubation temperature group were further split into three temperature groups in a full-factorial way for LPS challenge. In total, nine temperature groups (three incubation temperatures x three challenge temperatures) were generated. At 24 h post LPS challenge, mortality of larvae were recorded. Larvae originating from 24 °C incubation temperature group had higher mortality rate than larvae from the other two temperature groups. LPS-treated larvae from three temperature groups, incubation 24 °C x challenge 24 °C, incubation 24 °C x challenge 32 °C, and incubation 32 °C x challenge 24 °C, together with their respective control were chosen for transcriptomic analyses using mRNA sequencing. A total of 722 genes were determined differentially expressed (DEGs) by DESeq2 (adjusted p-value < 0.05) in LPS-challenged larvae compared to control, and 605 of them had a fold change greater than 1.5, including 294 DEGs (144 up-/150 down-regulated) in larvae incubated and challenged with LPS at 24 °C; 33 DEGs (20 up-/13 down-regulated) in larvae incubated at 32 °C and challenged at 24 °C; and 278 DEGs (190 up-/88 down-regulated) in larvae incubated at 24 °C and challenged at 32 °C. Larvae incubated and challenged with LPS at 24 °C had stimulated innate immune response compared to control, while they also showed down-regulated innate immune processes and genes. In larvae incubated at 32 °C and challenged at 24 °C, the innate immune processes were up-regulated in larvae exposed to LPS compared to control, and theses processes were even much stronger (with higher enrichment values) than larvae from incubation and challenge temperature of 24 °C. In larvae incubated at 24 °C and challenged with LPS at 32 °C, limited innate immune response were up-regulated, and additional hypoxia and oxidative processes were observed. Genes annexin A2a, S100 calcium binding protein A10b, and lymphocyte antigen-6, epidermis were identified as promising candidates for LPS recognition and signal transduction.
Publication Title
Low incubation temperature during early development negatively affects survival and related innate immune processes in zebrafish larvae exposed to lipopolysaccharide.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Mus musculus
- 13 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Pseudoautosomal regions (PAR1 and PAR2) in eutherians retain homologous regions between the X and Y chromosomes that play a critical role in the obligatory X-Y crossover during male meiosis. Genes that reside in the PAR1 are exceptional in that they are rich in repetitive sequences and undergo a very high rate of recombination. Remarkably, murine PAR1 homologs have translocated to various autosomes, reflecting the complex recombination history during the evolution of the mammalian X chromosome. We now report that the SNF2-type chromatin remodeling protein ATRX controls the expression of eutherians ancestral PAR1 genes that have translocated to autosomes in the mouse. In addition, we have identified two potentially novel mouse PAR1 orthologs. We propose that the ancestral PAR1 genes share a common epigenetic environment that allows ATRX to control their expression.
Publication Title
The SWI/SNF protein ATRX co-regulates pseudoautosomal genes that have translocated to autosomes in the mouse genome.
Sample Metadata Fields
Sex
View Samples- Homo sapiens
- 6 Downloadable Samples
- Illumina HiSeq 2500
Description
Current pipelines used to map genetrap insertion sites are based on inverse- or splinkerette-PCR methods, which despite their efficacy are prone to artifacts and do not provide information on the impact of the genetrap on the expression of the targeted gene. We developed a new method, which we named TrapSeq, for the mapping of genetrap insertions based on paired-end RNA sequencing. By recognizing chimeric mRNAs containing genetrap sequences spliced to an endogenous exon, our method identifies insertions that lead to productive trapping. Overall design: We conducted two independent screenings for sensitivity against 6-thioguanine (6TG) and an ATR inhibitor (ATRi). We applied our RNAseq-based pipeline (TrapSeq) to identify mutations that provide resistance to these reagents. Importantly, and besides its use for screenings, when applied to individual clones our method provides a fast and cost-effective way that not only identifies the insertion site of the genetrap but also reveals the impact of the insertion on the expression of the trapped gene. Please note that HAP1, haploid for all chromosomes, derives from near-haploid KBM7 parent line which was in turn obtained from a chronic myeloid leukemia patient in blast crisis phase (Carette et al. Nature 477:340-343, 2011).
Publication Title
Trap<sup>Seq</sup>: An RNA Sequencing-Based Pipeline for the Identification of Gene-Trap Insertions in Mammalian Cells.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Homo sapiens
- 70 Downloadable Samples
- Illumina HiSeq 2500
Description
We report the application of RNA-Seq analysis to determine the transcriptional responses to Mn dose, ranging from physiological to toxicological levels in human SH-SY5Y neuroblastoma cells. We find that Mn dose showed widespread effects in abundance of protein coding genes for metabolism of reactive oxygen species, energy sensing, glycolysis, protein homeostasis including the unfolded protein response and transcriptional regulation. Adaptive responses at physiological Mn concentration-10 µM Mn for 5 h, a concentration that did not result in cell death after 24 h increased abundance of differentially expressed genes (DEGs) in the protein secretion pathway that function in protein trafficking and cellular homeostasis.These include BET1 (Golgi vesicular membrane trafficking protein), ADAM10 (ADAM metallopeptidase domain 10) and ARFGAP3 (ADP-ribosylation factor GTPase activating protein 3). In contrast, 5 h exposure to 100 µM Mn, a concentration that caused cell death after 24 h, increased abundance of DEGs for components of the mitochondrial oxidative phosphorylation pathway. In conclusion, this study provides a framework for Mn dose dependent exposure in a human in vitro cell culture model and provides a testable hypothesis for in vivo studies. Importantly, the transcriptome responses at toxic Mn dose demonstrated patterns observed with neurological diseases and suggest that differential functions of the secretory pathway and mitochondria could provide a basis to improve detection and management of adverse environmental and occupational Mn exposures. Overall design: Examination of transcriptomic responses to Mn dose (0,1,5,10,50,100 µM MnCl2 for 5 h) in human SH-SY5Y neuroblastoma cells with three biological replicates per Mn treatment using Illumina HiSeq 2500.
Publication Title
Transcriptome Analysis Reveals Distinct Responses to Physiologic <i>versus</i> Toxic Manganese Exposure in Human Neuroblastoma Cells.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples