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Danio rerio
14 Downloadable Samples
IlluminaHiSeq1000
Description
RNA-seq data from control and MCT8 morphant zebrafish embryos at 25hpf
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 9 Downloadable Samples
- Illumina HiSeq 4000
Description
To get a deeper understanding of molecular mechanism elicited by alogliptin intervention, high-throughput RNA sequencing (RNA-seq) of the expression levels of all genes in the liver was performed
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part
View Samples- Homo sapiens
- 8 Downloadable Samples
- IlluminaHiSeq2000
Description
Despite many years of study of inversions, very little is known about their functional consequences, especially in humans. A common hypothesis is that the selective value of inversions stems in part from their effects on nearby genes, although evidences of this in natural populations are almost nonexistent. Here we present a global analysis of a new 415-kb polymorphic inversion that is among the longest ones found in humans and is the first with clear position effects. This inversion is located in chromosome 19 and has been generated by non-homologous end joining between blocks of transposable elements with low identity. PCR genotyping in 541 individuals from eight different human populations allowed the detection of tag SNPs and inversion genotyping in multiple worldwide populations, showing that the inverted allele is mainly found in East-Asia with an average frequency of 4.7%. Interestingly, one of the breakpoints disrupts the transcription factor gene ZNF257, causing a significant reduction in the total expression level of this gene in lymphoblastoid cell lines. RNA-Seq analysis of the effects of this expression change in standard homozygotes and inversion heterozygotes revealed distinct expression patterns that were validated by quantitative RT-PCR. Moreover, we have found a new fusion transcript that is generated exclusively from inverted chromosomes around one of the breakpoints. Finally, by the analysis of the associated nucleotide variation, we have estimated that the inversion was generated approximately 43,450 years ago and, while a neutral evolution cannot be ruled out, its current frequencies are more consistent with those expected for a deleterious variant, although no significant association with phenotypic traits has been found so far.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Danio rerio
- 17 Downloadable Samples
Affymetrix Zebrafish Genome Array (zebrafish)
Description
microRNAs play crucial roles in the early development of an organism. However the regulation of transcription through the action of microRNAs during the initial embyonic development has not been studied.
Publication Title
miR-34 is maternally inherited in Drosophila melanogaster and Danio rerio.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The proinflammatory cytokine, TNFalpha is critical in maintaining liver homeostasis since it is a major determiner of hepatocyte life and death. Considering this, gene transcription profiling was examined in control and TNFalpha treated HepG2 cells. Results indicated that TNFalpha could significantly alter the expression of a significant number of genes; most of them were functionally distributed among molecular functions like catalytic activity, binding, molecular transducer activity, transporter activity, translation and transcription regulator activities or enzyme regulator activity. Also, within genes up-regulated by TNFalpha, several GO terms related to lipid and fat metabolism were significantly overrepresented indicating global dysregulation of fat metabolism within the hepatocyte and those within the down-regulated dataset included genes involved in immunoglobulin receptor activity and IgE binding thereby indicating a compromise in immune defense mechanism(s) apart from those involved the DNA binding and protein binding categories. The interacting network of lipid metabolism, small molecule biochemistry was derived to be significantly affected that correlated well with the top canonical pathway of biosynthesis of steroids and molecular and cellular function of lipid metabolism. All these indicate TNFalpha to be significantly altering the transcriptome profiling within HepG2 cells with genes involved in lipid and steroid metabolism being the most favoured. This study suitably addresses the genes that determine TNFalpha mediated alterations within the hepatocyte mainly the phenotypes of hepatic steatosis and fatty liver that are associated with several hepatic pathological states.
Publication Title
Gene expression profiling and network analysis reveals lipid and steroid metabolism to be the most favored by TNFalpha in HepG2 cells.
Sample Metadata Fields
No sample metadata fields
View Samples- Bos indicus
- 4 Downloadable Samples
- Affymetrix Bovine Genome Array (bovine)
Description
Hypobaric Hypoxia Induced Transcriptional profiling of Bovine (Bos indicus)
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part, Disease, Disease stage, Subject
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SRP168448- Mus musculus
- 12 Downloadable Samples
- Illumina HiSeq 3000
Description
The expression of lncRNAs in the hypothalamic neuronal stem cells of young mice and aged mice.The expression pattern of mRNAs in the hypothalamic neuronal stem cells of aged Hnscr null mice and littermate wild-type mice.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Cell line, Treatment
View Samples- Homo sapiens
- 132 Downloadable Samples
Description
In 2014 Western Africa experienced an unanticipated explosion of infections with Ebola virus (EBOV). What distinguishes fatal from non-fatal outcomes remains largely unknown, yet is key to optimising personalised treatment strategies. Here transcriptome data for peripheral blood taken from infected and convalescent, recovering patients, was used to identify early stage host factors that were associated with acutely ill patients that ultimately either survived or succumbed to the disease.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 6 Downloadable Samples
- Illumina HiSeq 2500
Description
Statins, the cholesterol lowering agents, can increase diabetes incidence and impair glucose tolerance via its detrimental effects on non-hepatic tissues, such as pancreatic islet, but underlying mechanism has not been clarified. In atorvastatin-treated high fat diet mice, we found reduced pancreatic ß-cell size, ß-cell mass, mature insulin granules and reduced insulin secretion along with the deteriorated glucose tolerance. Transcriptome profiling of primary pancreatic islets showed inhibitory effects of atorvastatin on expression of genes encoding key pancreatic transcription factors, mTOR signaling pathway and small G proteins (sGPs).
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part, Cell line, Treatment
View Samples- Homo sapiens
- 26 Downloadable Samples
- Illumina HumanHT-12 V4.0 expression beadchip
Description
Extrapulmonary manifestations constitute 15-20% of tuberculosis cases, with lymph node as the most common site. Understanding of disease etiology is limited due to the lack of understanding patients infected tissue milieu. This study was designed to perform global transcriptome analysis of lymph node tissues from healthy individuals and Mycobacterium tuberculosis infected lymph nodes of patients to decipher the local response of infected tissue.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part, Disease
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