Project description:Transcriptional profiling of C. elegans first larval stage whole animals comparing lin-35(n745) mutants and lin-35(n745) treated with mes-4(RNAi) at 26 degrees. One-condition experiment, mutant (lin-35) vs. mutant plus RNAi (lin-35, mes-4RNAi). Biological replicates 4 mutant, 4 mutant plus RNAi harvested indepedently. One lin-35 replicate and one lin-35, mes-4(RNAi) replicate per array.
Project description:We classified samples and deciphered a key genes signature of intratumor heterogeneity by Principal Component Analysis and Weighted Gene Co-expression Network Analysis. At the genome level, we identified common GB copy number alterations and but a strong inter-individual molecular heterogeneity.
Project description:Transcriptional profiling of C. elegans first larval stage whole animals comparing lin-35(n745) mutants and N2 (wild type) at 26 degrees. One-condition experiment, mutant (lin-35) vs. WT. Biological replicates 4 mutant, 4 wildtype harvested indepedently. One lin-35 replicate and one WT replicate per array.
Project description:To identify substrates of the ubiquitinating E3 enzyme Rsp5 we applied purified Rsp5 to duplicate protein arrays. The Rsp proteins were expressed as fusion proteins to GST. We used as a control Ubr1, a RING domain containing E3 ligase We analyzed Rsp5 from S.cerevisiae on duplicate arrays, with four control chips, two without Rsp5 and two with Ubr1.
Project description:This dataset contains 48 RNA-seq samples from Triticum aestivum cv. Paragon plants grown under field conditions as part of the WGIN 2016 diversity trial. Flag leaf node tissues were harvested at eight time points following anthesis to capture transcriptional changes associated with senescence progression. Plants were subjected to two nitrogen fertilisation treatments (100 and 200 kg N ha⁻¹), with three biological replicates per treatment and time point. The selected time points for each nitrogen level were: N100 – 0, 7, 14, 21, 25, 28, 31, and 34 days post-anthesis (DPA); N200 – 0, 7, 14, 21, 28, 32, 35, and 38 DPA. This time-course RNA-seq dataset enables the investigation of gene expression dynamics during post-anthesis senescence in wheat flag leaf nodes, which serve as central hubs for nutrient trafficking during grain filling.
Project description:Microarray-based expression profiling of dissected gonads from efl-1, dpl-1 and lin-35 mutants reveals that EFL-1 and DPL-1 promote expression of an extensively overlapping set of target genes, consistent with the expectation that these two proteins function as a heterodimer. Regulatory regions upstream of many of these target genes have a canonical E2F binding site, suggesting that their regulation by EFL-1/DPL-1 is direct. Many EFL-1/DPL-1 responsive genes encode proteins required for oogenesis and early embryogenesis, rather than cell cycle components. By contrast, LIN-35 appears to function primarily as a repressor of gene expression in the germ line, and the genes that it acts on are for the most part distinct from those regulated by EFL-1 and/or DPL-1 We isolated dissected gonads from dpl-1, efl-1 and lin-35 mutant adults and compared each to control dissected gonads. RNA was linearly amplified prior to labeling for all genotypes. Each comparison was done in triplicate (dpl-1 and lin-35) or in quadruplicate (efl-1) on independently grown and isolated animals.
Project description:A cell line representative of human high-grade serous ovarian cancer (HGSOC) should not only resemble its tumor of origin at the molecular level, but also demonstrate functional utility in pre-clinical investigations. Here we report the integrated proteomic analysis of 26 ovarian cancer cell lines, HGSOC tumors, immortalized ovarian surface epithelial cells, and fallopian tube epithelial cells via a single-run mass spectrometric workflow. The in-depth quantitation of > 10,000 proteins results in three distinct cell line categories: epithelial (group I), clear cell (group II), and mesenchymal (group III). We identify a 67-protein cell line signature, which separates our entire proteomic dataset, as well as a confirmatory publicly available CPTAC/TCGA tumor proteome dataset, into a predominantly epithelial and mesenchymal HGSOC tumor cluster. This proteomics-based epithelial/mesenchymal stratification of cell lines and human tumors indicates a possible origin of HGSOC either from the fallopian tube or from the ovarian surface epithelium.
Project description:We report an integrated analysis incorporating DNA copy number analyses, somatic exon mutations, mRNA expression via RNA-sequencing, and shotgun mass spectrometry analysis of protein abundance in 108 surgically resected squamous cell lung cancers (SCC) with accompanying clinical outcome, evaluation of tumor pathology, and other clinically relevant data. We identified three major subtypes of SCC at the proteomic level, with two groups associated with inflammation/immune response or oxidation-reduction biology. Inflamed tumors could be further sub-classified based on neutrophil infiltration or antigen presentation proteomes and reflected patterns of infiltrating immune cells. No gene mutations, mRNA signatures, or proteomic subclasses were associated with outcomes; however, the presence of B-cell rich tertiary lymph node structures could be associated with better patient outcomes. By integrating our proteogenomic data with publicly available RNA interference screen data, we identified TP63, PSAT1, and AKR1C3 as vulnerabilities in SCC, particularly in the redox proteomic group. This cohort and its deep molecular data serves as an important resource to better understand biology and targets associated with SCC.
Project description:Mitochondrial DNA encodes thirteen subunits of the oxidative phosphorylation (OXPHOS) system, which are synthesized inside the organelle and essential for cellular energy supply. How mitochondrial gene expression is regulated and integrated into cellular physiology is little understood. Here, we performed a high-throughput screen combining fluorescent-labelling of mitochondrial translation products with siRNA-mediated knockdown, to identify cellular kinases regulating translation. As proof of principle, the screen identified known kinases that affect mitochondrial translation, and it also revealed several kinases not yet linked to this process. Among the latter, we focused on the primarily cytosolic kinase FN3K, which localizes partially to mitochondria, to support translation. Mass spectrometric (MS) bottom-up analysis of peptide samples after FN3K-flag immunoisolation in isolated mitochondria (transfected with FN3K-flag plasmid) enabled the identification of several proteins of the mitochondrial ribosome to be interacting with FN3K. Further experiments showed that FN3K likely modulates the assembly of mitochondrial ribosomes, thereby affecting translation. Overall, our work provides a reliable approach to identify new protein functions for mitochondrial gene expression, in a high throughput manner.
Project description:Colorectal cancers (CRC) with deficient mismatch repair (dMMR) exhibit variable responses to immune checkpoint inhibitors, despite their immunogenic nature. To investigate the molecular basis of this heterogeneity, we performed integrated bulk RNA sequencing and immune repertoire profiling on tumor and adjacent normal mucosa from treatment-naïve dMMR CRC patients. Using weighted gene co-expression network analysis, we identified transcriptional modules associated with T and B cell clonality, immune-metabolic interactions, and therapeutic responsiveness. Our dataset provides a valuable resource for understanding the tumor microenvironment in dMMR CRC and supports the development of biomarkers for patient stratification beyond mismatch repair status.