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GSE49795
Homo sapiens
3 Downloadable Samples
Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Case story. A patient with massive infiltration of the visceral adipose tissue depot by BAT in a patient with a catecholamine secreting paraganglioma. BAT tissue was identified by protein expression of UCP1 (western blotting and immunostaining)
Publication Title
Chronic adrenergic stimulation induces brown adipose tissue differentiation in visceral adipose tissue.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 14 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
We have derived hESC from biopsied blastomeres of cleavage stage embryos under virtually the same conditions we used for the derivation of hESC lines from inner cell mass of blastocyst stage embryos. Blastomere-derived hESC lines exhibited all the standard characteristics of hESC including undifferentiated proliferation, genomic stability, expression of pluripotency markers and the ability to differentiate into the cells of all three germ layers both in vitro and in vivo. To examine whether hESC lines derived from two developmental stages of the embryo differ in gene expression, we have subjected three blastomere-derived hESC lines and two ICM-derived hESC lines grown under identical culture conditions to transcriptome analysis using gene expression arrays. Unlike previously reported comparisons of hESC lines which demonstrated, apart from core hESC-associated pluripotency signature, significant variations in gene expression profiles of different lines, our data show that hESC lines derived and grown under well-controlled defined culture conditions adopt nearly identical gene expression profiles. Moreover, blastomere-derived and ICM-derived hESC exhibited very similar transcriptional profiles independent of the developmental stage of the embryo from which they originated. Furthermore, this profile was evident in very early passages of the cells and did not appear to be affected by extensive passaging. These results suggest that during derivation process cells which give rise to hESC acquire virtually identical stable phenotype and are not affected by the developmental stage of the starting cell population.
Publication Title
Human embryonic stem cells derived from embryos at different stages of development share similar transcription profiles.
Sample Metadata Fields
Specimen part, Disease, Cell line
View Samples- Bos taurus
- 39 Downloadable Samples
- Affymetrix Bovine Genome Array (bovine)
Description
Mycobacterium bovis is an intracellular pathogen that causes tuberculosis in cattle. Following infection, the pathogen resides and persists inside host macrophages by subverting host immune responses via a diverse range of mechanisms. Here, a high-density bovine microarray platform was used to examine the bovine monocyte-derived macrophage transcriptome response to M. bovis infection relative to infection with the attenuated vaccine strain, M. bovis Bacille CalmetteGurin. Differentially expressed genes were identified (adjusted P-value 0.01) and interaction networks generated across an infection time course of 2, 6 and 24 h. The largest number of biological interactions was observed in the 24 h network, which exhibited small-worldscale-free network properties. The 24 h network featured a small number of key hub and bottleneck gene nodes, including IKBKE, MYC, NFKB1 and EGR1 that differentiated the macrophage response to virulent and attenuated M. bovis strains, possibly via the modulation of host cell death mechanisms. These hub and bottleneck genes represent possible targets for immunomodulation of host macrophages by virulent mycobacterial species that enable their survival within a hostile environment.
Publication Title
Key Hub and Bottleneck Genes Differentiate the Macrophage Response to Virulent and Attenuated Mycobacterium bovis.
Sample Metadata Fields
Sex, Age, Specimen part, Treatment, Time
View Samples- Bos taurus
- 16 Downloadable Samples
- Affymetrix Bovine Genome Array (bovine)
Description
Background: Mycobacterium bovis is the causative agent of bovine tuberculosis (BTB), a pathological infection with significant economic impact. Recent studies have highlighted the role of functional genomics to better understand the molecular mechanisms governing the host immune response to M. bovis infection. Furthermore, these studies may enable the identification of novel transcriptional markers of BTB that can augment current diagnostic tests and surveillance programmes. In the present study, we have analysed the transcriptome of peripheral blood leukocytes (PBL) from eight M. bovis-infected and eight control non-infected age-matched and sex-matched Holstein-Friesian cattle using the Affymetrix GeneChip Bovine Genome Array with features representing more than 23,000 gene transcripts and over 19,000 gene probe sets.
Publication Title
Genome-wide transcriptional profiling of peripheral blood leukocytes from cattle infected with Mycobacterium bovis reveals suppression of host immune genes.
Sample Metadata Fields
Sex, Specimen part
View Samples- Bos taurus
- 77 Downloadable Samples
Illumina HiSeq 2000
Description
Mycobacterium bovis, the agent of bovine tuberculosis, causes an estimated $3 billion annual losses to global agriculture due, in part, to the limitations of current diagnostics. Development of next-generation diagnostics requires a greater understanding of the interaction between the pathogen and the bovine host. Therefore, to explore the early response of the alveolar macrophage to infection, we report the first application of RNA-sequencing to define, in exquisite detail, the transcriptomes of M. bovis-infected and non-infected alveolar macrophages from ten calves at 2, 6, 24 and 48?hours post-infection. Differentially expressed sense genes were detected at these time points that revealed enrichment of innate immune signalling functions, and transcriptional suppression of host defence mechanisms (e.g., lysosome maturation). We also detected differentially expressed natural antisense transcripts, which may play a role in subverting innate immune mechanisms following infection. Furthermore, we report differential expression of novel bovine genes, some of which have immune-related functions based on orthology with human proteins. This is the first in-depth transcriptomics investigation of the alveolar macrophage response to the early stages of M. bovis infection and reveals complex patterns of gene expression and regulation that underlie the immunomodulatory mechanisms used by M. bovis to evade host defence mechanisms. Overall design: Whole-transcriptome analysis of M. bovis- and non-infected alveolar macrophages from ten calves (n = 10) at 2, 6, 24 and 48 hours (h) post-infection using RNA-sequencing (RNA-seq).
Publication Title
RNA sequencing provides exquisite insight into the manipulation of the alveolar macrophage by tubercle bacilli.
Sample Metadata Fields
Sex, Specimen part, Subject, Time
View Samples- Bos taurus
- 48 Downloadable Samples
- Affymetrix Bovine Genome Array (bovine)
Description
Background: Mycobacterium bovis, the causative agent of bovine tuberculosis, is a major cause of mortality in global cattle populations. Macrophages are among the first cells types to encounter M. bovis following exposure and the response elicited by these cells is pivotal in determining the outcome of infection. Here, a functional genomics approach was undertaken to investigate global gene expression profiles in bovine monocyte-derived macrophages (MDM) purified from seven age-matched non-related females, in response to in vitro challenge with M. bovis (multiplicity of infection 2:1). Total cellular RNA was extracted from non-challenged control and M. bovis-challenged MDM for all animals at intervals of 2 hours, 6 hours and 24 hours post-challenge and prepared for global gene expression analysis using the Affymetrix GeneChip Bovine Genome Array.
Publication Title
Global gene expression and systems biology analysis of bovine monocyte-derived macrophages in response to in vitro challenge with Mycobacterium bovis.
Sample Metadata Fields
Sex, Age, Specimen part, Time
View Samples- Homo sapiens
- 77 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
We have carried out whole-genome expression profiling of whole blood from obese subjects, defined as obese diet-sensitive and obese diet-resistant, and well matched lean individuals. The diet-sensitive or diet-resistant status refers to the different rates of weight loss observed in the two groups on a low-calorie diet regimen. Bioinformatic analysis revealed alterations in transcription in key pathways that are consistent with impaired capacity for fatty acid oxidation driven mitochondrial ATP synthesis in obese subjects who are resistant to weight loss.
Publication Title
Gene expression profiling in whole blood identifies distinct biological pathways associated with obesity.
Sample Metadata Fields
Sex, Subject, Time
View Samples- Homo sapiens
- 27 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
To investigate the role of p53 and DICER in the induction of ER stress, wildtype, p53 knockout or DICER mutant HCT116 colon cancer cells were treated with the ER stress inducers tunicamycin or brefeldin A for 24 hours.
Publication Title
A close connection between the PERK and IRE arms of the UPR and the transcriptional regulation of autophagy.
Sample Metadata Fields
Cell line, Treatment
View Samples- Homo sapiens
- 19 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
We profiled gene expression at the maternal-fetal interface during the second trimester of pregnancy (13-22 wks) in trisomy 13 (T13; Patau syndrome, n = 4), trisomy 18 (T18; Edwards syndrome, n = 4), trisomy 21 (T21; Down syndrome, n = 8), and in euploid pregnancies (n = 4). FISH confirmed the ploidy of the samples. Global transcriptional profiling identified differentially expressed transcripts ( 2-fold) in T21 (n = 160), T18 (n = 80), and T13 (n = 125). The majority were upregulated. Unexpectedly, most of the misexpressed genes were not located on the relevant trisomic chromosome, suggesting genome-wide dysregulation. A much smaller proportion of the differentially expressed transcripts were encoded on the aneuploid chromosome, also implicating gene dosage (1-5). In T21, <10% of the genes were transcribed from that chromosome, all but one from the Down syndrome critical region (21q21-22), which is postulated to play an important role in the clinical phenotype. For T13 and T18, a higher proportion of the overexpressed genes were located on the trisomic chromosome. In T13, 15% of the upregulated genes were on the affected chromosome; 15 resided on the long arm, 13q11-14. In T18, the percentage increased to 24, 15 of which were also located on the long arm (18q11-22). Our data suggested that the placental (and possibly fetal) phenotypes that are associated with T13, T18 and T21 are driven by the combined effects of genome-wide phenomena and increased gene dosage from critical regions of the triploid chromosome.
Publication Title
Placental transcriptomes in the common aneuploidies reveal critical regions on the trisomic chromosomes and genome-wide effects.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 16 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Transcriptomic characterization of cultured primary human cytrophoblasts (2nd trimester) undergoing differentiation/invasion in vitro.
Publication Title
Transcriptional Dynamics of Cultured Human Villous Cytotrophoblasts.
Sample Metadata Fields
Specimen part
View Samples