Sample Prep -EHP
Ontology highlight
ABSTRACT:
INSTRUMENT(S): QE-HF
ORGANISM(S): Xenopus <genus> (ncbitaxon:8353)
SUBMITTER: 
Norman J. Dovichi
PROVIDER: MSV000081691 | MassIVE | Wed Nov 08 06:28:00 GMT 2017
REPOSITORIES: MassIVE
Similar Datasets
Project description:DOI: 10.1007/s00216-016-0122-8
Evaluation of PrinCE autosampler
2017-11-08 | MSV000081688 | MassIVE
Project description:Ex vivo colorectal adenocarcinoma samples were analysed by desorption electrospray ionisation using an Orbitrap mass spectrometer. The samples were analysed in negative mode over the m/z range 600-1000. Some of the samples presented in this dataset were analysed as part of [1]. The study makes available imzML files of profile and centroid mode data, as well as low- and high- resolution optical image files of H&E-stained sections. These files can be found in the zip file named after each tissue section. </p> Ref:</br> [1] Gerbig S, Golf O, Balog J, Denes J, Baranyai Z, Zarand A, Raso E, Timar J, Takats Z. Analysis of colorectal adenocarcinoma tissue by desorption electrospray ionization mass spectrometric imaging. Anal Bioanal Chem. 2012 Jun;403(8):2315-25. doi:10.1007/s00216-012-5841-x. PMID:22447214</br>
2016-04-28 | MTBLS289 | MetaboLights
Project description:Collaboration between Iowa and Notre Dame. Proteomic data was ran at ND.
2017-11-08 | MSV000081690 | MassIVE
Project description:Taking the advantage that B16F10 cells retain the wild-type p53, we introduced the p53 partner into these cells, the p19Arf. Also, in order to induce a immune stimulation in experiments *in vivo*, we introduced the interferon-beta cDNA. This combination induced several benefits when compared to the use of these factors alone, as seen by propidium iodide staining, tunel staining, several gene expression analysis, tumor growth, mice survival, among others. Because of this, we had the interest to study the effects of the combination of p19Arf plus interferon-beta upon gene regulation of B16F10 cells, compared to the effects of these transgenes alone. Previous works from our group that show several benefits of p19Arf plus interferon-beta combination upon B16F10 cells are described in Merkel et al (2010) doi: 10.1186/1471-2407-10-316, Merkel et al (2013) doi:10.1038/cgt.2013.23 and Medrano et al (2016) doi: 10.1007/s00262-016-1807-8 .
2017-12-02 | E-MTAB-5399 | biostudies-arrayexpress
Project description:Fungal effectors play important roles in inciting disease development on host plants. We identified an effector (Secreted in Xylem4, SIX4) in an Arabidopsis infecting isolate (Fo5176) of the root-infecting fungal pathogen Fusarium oxysporum and demonstrated this effector is required for full virulence. To explore the role of Fo5176_SIX4 we use whole transcriptome profiling of root tissues from plants overexpressing this effector (35sSIX4) versus wild-type (Col-0) plants after F. oxysporum infection. Published in DOI:10.1007/978-3-319-42319-7_4. Belowground Defence Strategies in Plants.
2016-05-31 | GSE75928 | GEO
Project description:Neighborhood disadvantage (ND) is associated with shorter breast cancer (BCa) survival. Although studies have identified that ND is associated with alterations in DNA methylation (DNAme) or gene expression, a comprehensive study integrating DNAme with coding (mRNA) and non-coding (miRNA, tRNA) transcriptomic data to understand how the epigenome regulates key biological pathways is lacking. DNAme, mRNA, miRNA, and tRNA-derived fragment data were analyzed from 80 ER+/HER2- BCa samples from Hispanic White women with no significant differences in genetic ancestry, BMI, smoking, alcohol, Oncotype DX scores, and stage. We analyzed the association between objective ND [Area Deprivation Index (ADI)], subjective ND [Neighborhood Social Environment Adversity Survey (NSEAS)], DNAme, coding, and non-coding data to understand how the epigenome regulates key biological pathways among women living in ND. The cohort was divided into neighborhood advantage (NA, ADI<5; n=55, 69%) and ND (ADI≥5; n=25, 31%). In tumors from ND, calcium signaling and cell adhesion pathways were hypermethylated, immune-related pathways hypomethylated, immune response genes upregulated, and estrogen response genes downregulated. Small RNA analysis showed differential expression of miRNA isoforms and tRNA-derived fragments related to ND. Subjective ND correlated with epigenetic changes in calcium signaling, cell adhesion, and metabolic pathways, along with upregulation of proliferative and stemness pathways. We discovered novel associations between ND and epigenomic regulation of key clinically relevant oncogenesis pathways associated with aggressive biology, such as estrogen response pathways. These findings lay the foundation for multi-institutional studies to validate our findings and guide future treatment and cancer control interventions.
2025-08-15 | GSE290735 | GEO
Project description:Neighborhood disadvantage (ND) is associated with shorter breast cancer (BCa) survival. Although studies have identified that ND is associated with alterations in DNA methylation (DNAme) or gene expression, a comprehensive study integrating DNAme with coding (mRNA) and non-coding (miRNA, tRNA) transcriptomic data to understand how the epigenome regulates key biological pathways is lacking. DNAme, mRNA, miRNA, and tRNA-derived fragment data were analyzed from 80 ER+/HER2- BCa samples from Hispanic White women with no significant differences in genetic ancestry, BMI, smoking, alcohol, Oncotype DX scores, and stage. We analyzed the association between objective ND [Area Deprivation Index (ADI)], subjective ND [Neighborhood Social Environment Adversity Survey (NSEAS)], DNAme, coding, and non-coding data to understand how the epigenome regulates key biological pathways among women living in ND. The cohort was divided into neighborhood advantage (NA, ADI<5; n=55, 69%) and ND (ADI≥5; n=25, 31%). In tumors from ND, calcium signaling and cell adhesion pathways were hypermethylated, immune-related pathways hypomethylated, immune response genes upregulated, and estrogen response genes downregulated. Small RNA analysis showed differential expression of miRNA isoforms and tRNA-derived fragments related to ND. Subjective ND correlated with epigenetic changes in calcium signaling, cell adhesion, and metabolic pathways, along with upregulation of proliferative and stemness pathways. We discovered novel associations between ND and epigenomic regulation of key clinically relevant oncogenesis pathways associated with aggressive biology, such as estrogen response pathways. These findings lay the foundation for multi-institutional studies to validate our findings and guide future treatment and cancer control interventions.
2025-08-15 | GSE290736 | GEO
Project description:Neighborhood disadvantage (ND) is associated with shorter breast cancer (BCa) survival. Although studies have identified that ND is associated with alterations in DNA methylation (DNAme) or gene expression, a comprehensive study integrating DNAme with coding (mRNA) and non-coding (miRNA, tRNA) transcriptomic data to understand how the epigenome regulates key biological pathways is lacking. DNAme, mRNA, miRNA, and tRNA-derived fragment data were analyzed from 80 ER+/HER2- BCa samples from Hispanic White women with no significant differences in genetic ancestry, BMI, smoking, alcohol, Oncotype DX scores, and stage. We analyzed the association between objective ND [Area Deprivation Index (ADI)], subjective ND [Neighborhood Social Environment Adversity Survey (NSEAS)], DNAme, coding, and non-coding data to understand how the epigenome regulates key biological pathways among women living in ND. The cohort was divided into neighborhood advantage (NA, ADI<5; n=55, 69%) and ND (ADI≥5; n=25, 31%). In tumors from ND, calcium signaling and cell adhesion pathways were hypermethylated, immune-related pathways hypomethylated, immune response genes upregulated, and estrogen response genes downregulated. Small RNA analysis showed differential expression of miRNA isoforms and tRNA-derived fragments related to ND. Subjective ND correlated with epigenetic changes in calcium signaling, cell adhesion, and metabolic pathways, along with upregulation of proliferative and stemness pathways. We discovered novel associations between ND and epigenomic regulation of key clinically relevant oncogenesis pathways associated with aggressive biology, such as estrogen response pathways. These findings lay the foundation for multi-institutional studies to validate our findings and guide future treatment and cancer control interventions.
2025-08-15 | GSE290733 | GEO
Project description:Processed and raw enteric adenovirus protein microarray reactivity data from 119 year-1 infant serum samples from a Bangladeshi birth cohort, with sample-level metadata aligned to Table 1 of the associated manuscript (Hendrick J, et al. J Infect Dis. 2025; jiaf558. doi:10.1093/infdis/jiaf558).
2025-12-28 | GSE314977 | GEO
Project description:Soil cultivation of spring wheat cultivar Remus. <br>
Hydroponic sampling of exudates to search for the BNI MBOA (and related compounds)<br>
Quantify MBOA<br>
Search for other known BNIS<br>
Characterize exudate<br>
<br>
LC-HRMS according to 10.1007/s00216-025-05818-y<br>
2026-01-08 | MSV000100411 | MassIVE