Projection-dependent ribosome profling from mouse mPFC.
Molecular and Circuit-Dynamical Identification of Top-Down Neural Mechanisms for Restraint of Reward Seeking.
Specimen part
View SamplesUsing anti-Argonaute (anti-AGO) antibody co-immunoprecipitation, followed by microarray analyses and downstream bioinformatics, RIP-Chip experiments enable direct analyses of miRNA targets. The analyses support four major findings: (i) RIP-Chip studies correlated with total input mRNA profiling provides more comprehensive information than using either RIP-Chip or total mRNA profiling alone after miRNA transfections; (ii) new data confirm that miR-107 paralogs target coding sequence (CDS) of mRNA; (iii) biochemical and computational studies indicate that the 3 portion of miRNAs plays a role in guiding miR-103/7 to the CDS of targets; and (iv) there are major sequence-specific targeting differences between miRNAs in terms of CDS versus 3-untranslated region targeting, and stable AGO association versus mRNA knockdown. For detailed protocol and for full discussion of the results please see Nelson PT et al, Nucleic Acids Res. 2011 Oct;39(18):8163-72.
Specific sequence determinants of miR-15/107 microRNA gene group targets.
Specimen part, Disease, Cell line
View SamplesCaesarean-delivered preterm pigs were fed 3 d of parenteral nutrition followed by 2 d of enteral formula feeding. Antibiotics (n=11) or control saline (n=13) were given twice daily from birth to tissue collection at d 5. NEC-lesions and intestinal structure, function, microbiology and immunity markers were recorded.
Antibiotics modulate intestinal immunity and prevent necrotizing enterocolitis in preterm neonatal piglets.
Specimen part, Treatment
View SamplesThe goal of this study is to identify downstream pathways, diagnostic markers, and potential therapeutic targets for IFS/CMN.
Mediators of receptor tyrosine kinase activation in infantile fibrosarcoma: a Children's Oncology Group study.
Specimen part
View SamplesBACKGROUND
Emmprin and survivin predict response and survival following cisplatin-containing chemotherapy in patients with advanced bladder cancer.
No sample metadata fields
View SamplesStaphylococcus aureus produces the cyclic dipeptides tyrvalin and phevalin (aureusimine A and B, respectively).
Phevalin (aureusimine B) production by Staphylococcus aureus biofilm and impacts on human keratinocyte gene expression.
Specimen part, Treatment
View SamplesWe sought to compare mRNA expression profiles between the parental SKOV3ip1 and taxane-resistant SKOV3TRip2 in order to determine what genes are mediating taxane resistance
Targeting aldehyde dehydrogenase cancer stem cells in ovarian cancer.
No sample metadata fields
View SamplesMORAB-003 significantly upregulated a number of genes involved in autophagic processing, including GABARAPL2, LC3II (MAP1LC3B), ATG3, ATG4B, and BECN1, while expression of the oncogenic factor PIK3C3 was downregulated.
Immunotherapy targeting folate receptor induces cell death associated with autophagy in ovarian cancer.
Specimen part, Cell line
View SamplesThe NEET proteins mitoNEET (mNT) and nutrient-deprivation autophagy factor-1 (NAF-1) are required for cancer cell proliferation and resistance to oxidative stress. MitoNEET and NAF-1 are also implicated in a number of other human pathologies including diabetes, neurodegeneration and heart disease, as well as in development, differentiation and aging. Previous studies suggested that mNT and NAF-1 could function in the same pathway in cancer cells, preventing the over-accumulation of iron and reactive oxygen species (ROS) in mitochondria. Nevertheless, it is unknown whether these two proteins interact in cells, and how they mediate their function. Here we demonstrate, using yeast two-hybrid, in vivo bimolecular fluorescence complementation (BiFC), direct coupling analysis (DCA), RNA- sequencing, ROS and iron imaging, and single and double shRNA lines with suppressed mNT, NAF-1 and mNT/NAF-1 expression, that mNT and NAF-1 interact in cancer cells and function in the same cellular pathway. We further show using an in vitro cluster transfer assay that mNT can transfer its clusters to NAF-1. Our study suggests that mNT and NAF-1 could function as part of an iron-sulfur (2Fe-2S) cluster relay to maintain the levels of iron and Fe-S clusters under control in the mitochondria of cancer cells, thereby preventing the activation of apoptosis and/or autophagy and thus promoting rapid cellular proliferation. Overall design: Examination of the effect of suppression of mNT in the breast cancer cell line MCF-7. Two sample types were analyzed, MCF-7 suppressed for mNT and MCF-7 Empty vector control, three replicates for each.
Interactions between mitoNEET and NAF-1 in cells.
Specimen part, Cell line, Subject
View SamplesGene expression profiling was carried out on peripheral blood mononuclear cell mRNA samples collected from renal cell carcinoma patients. The primary research question is whether gene expression differs as a function of patient's level of depression as measured by CESD score > 16.
Depressive symptoms and cortisol rhythmicity predict survival in patients with renal cell carcinoma: role of inflammatory signaling.
Specimen part, Disease
View Samples