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Rattus norvegicus
6 Downloadable Samples
Illumina HiSeq 2500
Description
Estrogens are traditionally considered to be female sex steroid hormones and most of the studies examining estrogen regulation of metabolic function in the liver have been conducted in females. However, the liver expresses high levels of estrogen receptor alpha (ESR1) in both males and females, which mediates the hepatic response to estrogens. In this study, we investigated whether metabolic disorders in Esr1 knockout (Esr1-/-) male rats were linked with loss of transcriptional regulation by ESR1 in liver. To identify the ESR1 regulated genes in the mutant liver, RNA-sequencing was performed on liver RNAs purified from young male rats. The raw data were analyzed using the CLC Genomics Workbench and high-quality RNA-sequencing reads were aligned to the Rattus norvegicus genome. Transcriptome data obtained from Esr1-/- liver RNAs were compared to that of wild type rats. Based on an absolute fold change of 2 with a p-value = 0.05, a total of 618 differentially expressed genes were identified in the Esr1-/- male liver. Pathway analyses demonstrated that the majority of differentially expressed genes are regulators of carbohydrate and lipid metabolism in the liver.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Disease, Cell line
View Samples- Rattus norvegicus
- 9 Downloadable Samples
- Illumina HiSeq 4000
Description
RNA seq analyses were performed in granulosa cells (GCs) collected from gonadotropin treated ESR2 mutant rats. Data obtained from a null mutant with Esr2 exon 3 deletion (?3) and another DNA binding domain (DBD) mutant with exon 4 deletion (?4) were compared to that of wildtype (WT) rats. The raw data were analyzed using CLC genomics workbench. High quality RNA-sequencing reads were aligned to the Rattus norvegicus genome. Differentially expressed genes in ?3 or ?4 Esr2-mutant GCs were identified based on the following criteria: FDR p-Value =0.05 and an absolute fold change of 2. Fewer differentially expressed genes were identified in ?3 compared to the ?4 mutant group. As both of the mutant groups demonstrated a common phenotype of ovulation failure, differentially expressed genes common to both in ?3 and ?4 mutant rats were emphasized and further analyzed in the companion article “ESR2 regulates granulosa cell genes essential for follicle maturation and ovulation” (Khristi et al., 2018).
Publication Title
ESR2 regulates granulosa cell genes essential for follicle maturation and ovulation.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 3 Downloadable Samples
- Illumina HiSeq 4000
Description
The goal of this study was to perform RNA-seq on postnatal day 12 mouse oocytes to quantify gene expression.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Disease, Cell line
View Samples- Homo sapiens
- 6 Downloadable Samples
- NextSeq 500
Description
RNA-sequencing analysis of RBP2 overexpressing MCF7 cell lines. RBP2 (also known as JARID1A), a member of the JARID1 family of histone H3 lysine K4 demethylases, has been considered to have an oncogenic potential in several cancer including breast cancer. Results provide insight into the transcriptional regulation of RBP2 in estrogen receptor positve breast cancer.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part, Disease, Cell line
View Samples
SRP076437- Homo sapiens
- 4 Downloadable Samples
- Illumina HiSeq 2000
Description
HLA-I positive and negative subpopulations isolated from human clear cell sarcoma xenografts
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Disease
View Samples- Mus musculus
- 2 Downloadable Samples
- Illumina Genome Analyzer IIx
Description
Dysfunction of Th17 cells leads to chronic inflammatory disorders. STAT3 orchestrates the expression of proinflammatory cytokinesand pathogenic cell differentiation from IL-17-producing Th17 cells. However, the pathways mediated by STAT3 signaling are not fully understood. Here, we observed that FRA1 and JUNB are directly involved in STAT3 binding to sites in the promoters of Fosl1 and Junb. Promoter binding increased expression of IL-17 and the development of Th17 cells. Overexpression of Fra1 and Junb in mice resulted in susceptibility to collagen-induced arthritis (CIA) and an increase in Th17 cell numbers and inflammatory cytokine production. In patients with rheumatoid arthritis (RA), FRA1 and JUNB were colocalized with STAT3 in the inflamed synovium. These observations suggest that FRA1 and JUNB are associated closely with STAT3 activation, and that this activation leads to Th17 cell differentiation in autoimmune diseases and inflammation.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Cell line
View Samples- Homo sapiens
- 12 Downloadable Samples
- Illumina HiSeq 1500
Description
MDA-MB-231 and T47D human breast cancer cells were chronically treated with the novel STAT3/5 inhibitor SH-4-54 for 60 and 30 days, respectively. Surviving treatment-resistant individual clones were isolated and characterized for their phosphorylated STAT3 and phosphorylated STAT5 status. 3 biological replicates of mRNA from a representative resistant clone derived from both MDA-MB-231 and T47D cells, in parallel with mRNA from their respective wild-type counterparts, was subjected to NextGeneration Sequencing to analyze changes in gene expression between untreated and resistant cells.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Cell line, Treatment
View Samples- Glycine max
- 5 Downloadable Samples
- Illumina HiSeq 2000
Description
Glycine max and Phytophthora sojae infected Glycine max Transcriptome
Publication Title
No associated publication
Sample Metadata Fields
Specimen part
View Samples- Glycine max
- 4 Downloadable Samples
- Illumina Genome Analyzer II
Description
The project was aim of search the different mechanism of resoonse to soybean cyst nematode and mining the candidate resisitance genes from next generation sequencing
Publication Title
No associated publication
Sample Metadata Fields
Specimen part, Disease, Disease stage
View Samples SRP059633- Homo sapiens
- 2 Downloadable Samples
- IlluminaHiSeq2000
Description
Intratumoral heterogeneity is common in all tumor types and major barrier against effective cancer therapy. Especially, human malignant mesothelioma that is an environmental contaminant- induced disease is known to be extremely heterogeneous with regards to morphology as well as molecular phenotypes, resulting in poor response to cancer therapy. This study was performed to investigate the global gene expression profile of distinct subpopulations of MS1, a human malignant mesothelioma cell line
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
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