Inhibition of IL6 signalling as a therapeutic strategy to eradicate cancer cells with chromosomal instability
Ontology highlight
ABSTRACT:
INSTRUMENT(S): NextSeq 500
ORGANISM(S): Homo sapiens
SUBMITTER: René Wardenaar
PROVIDER: E-MTAB-10923 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:RNA-sequencing samples from DMSO or Reversine treated hTERT RPE-1 cells. Reversine treated cells were further divided in those still able to continue to proliferate and those that got arrested. Cells were analyzed to generate panel in Figure 6d and e, and Extended Data Figure 8g and h.
2023-01-31 | E-MTAB-12537 | biostudies-arrayexpress
Project description:The advances in chemical proteomics have significantly expanded our understanding of the diversity and abundance of fatty-acylated proteins in eukaryotes, and reveal novel functions for these lipid protein modifications. Nonetheless, quantitative comparative proteomic analysis of fatty-acylated proteins in different cellular states is still challenging. To address these limitations, we systematically evaluated different proteomic methods (alk-16 chemical reporter and acyl-RAC) and established robust conditions to selectively and quantitatively profile fatty-acylated proteins in mammalian cells. Using a combination of metabolic labeling with fatty acid chemical reporters, selective chemical enrichment and label-free proteomics, we performed a quantitative analysis of fatty-acylated proteins in naïve and activated macrophages. These studies revealed novel fatty-acylated proteins associated with host immunity that are differently expressed and lipid-modified in different cellular states.
2018-03-28 | PXD003652 | Pride
Project description:Discover novel transcriptional units upstream of cell cycle genes Transcription of long noncoding RNAs (lncRNAs) within gene regulatory elements can modulate gene activity in response to external stimuli, but the scope and functions of such noncoding transcription are not known. Here we use an ultra-high density array that tiles the promoters of 56 cell cycle genes to interrogate 108 samples representing diverse perturbations. We identify 216 transcribed regions that encode putative lncRNAs--many of which have RT-PCR-validated periodic expression during the cell cycle, show altered expression in human cancers, and are regulated in expression by specific oncogenic stimuli, stem cell differentiation, or DNA damage. 53 samples tiled against respective controls
2011-05-21 | E-GEOD-28631 | biostudies-arrayexpress
Project description:RNA sequencing of medulloblastoma cell lines DAOY and USP13-med; wild type and VAPB KO.
2023-06-28 | E-MTAB-11914 | biostudies-arrayexpress
Project description:Immune checkpoint inhibitors (ICIs) are a type of cancer treatment that work by targeting molecules on immune cells that can inhibit the immune system's ability to attack cancer cells. One such checkpoint molecule is PD-1, which is found on the surface of T cells (a type of immune cell) and helps to prevent them from attacking healthy cells. When PD-1 binds to its ligand (a molecule on the surface of some cells), it sends a signal to the T cell to \\"turn off\\" and not attack the cell. This mechanism is important in preventing the immune system from attacking healthy cells, but it can also be exploited by cancer cells to avoid detection and destruction by the immune system. In this study YUMM2.1 mouse tumour cells were implanted subcutaneously. The effect of IFN-γ-pre-treatment, PARP14 inhibition and PD-1 antibody treatment are reported by RNA-seq.
2023-08-22 | E-MTAB-12872 | biostudies-arrayexpress
Project description:SUMO modification of proteins (sumoylation) is essential for mitotic progression from yeast to humans, but only a limited number of sumoylated proteins with functions in mitosis have been discovered. Vertebrates express three SUMO paralogs, SUMO-1, SUMO-2 and SUMO-3, but only SUMO-2 and -3 are chromosome-associated in mitosis. In this study, we used chromosome spreads to more precisely define the localization of endogenous SUMO-2 and -3 to the centromere as well as the chromosome protein scaffold. Furthermore, we developed methodologies for the immunopurification of endogenous SUMO-2 and -3 modified proteins from cell extracts. Using LC-MS/MS, we analyzed proteins immunopurified from mitotic chromosome fractions and G0 nuclear fractions. We identified 296 putative sumoylated proteins, with 138 being modified specifically in mitosis. We identified proteins known to localize to the centromere and kinetochore and the chromosome protein scaffold, consistent with SUMO-2/3 localization. Furthermore, we demonstrate that utilizing cell synchronization and fractionation allowed for the discovery of low abundance sumoylated proteins that are not detected in large asynchronous analyses. Our results provide a foundation for further characterization of the roles of sumoylation in regulating diverse aspects of chromosome segregation in mitosis. Thermo .raw files were uploaded to the ProHits (Liu et al, 2010) analytical suite and converted to .mzXML format using ReAdW software. Data were searched using X!Tandem (Craig & Beavis, 2004) against human ORFs (RefSeq v45). Search parameters specified a parent MS tolerance of +/- 15ppm, and an MS/MS tolerance of 0.4 Da, with up to two missed cleavages for trypsin. Oxidation of methionine and tryptophan, ubiquitylation of lysine, and alkylation of cysteine (by NEM) were allowed as variable modifications. Statistical validation of the results was performed using Peptide Prophet and Protein Prophet (Keller et al, 2002; Nesvizhskii et al, 2003) as part of the trans-proteomic pipeline. For each search, the Protein Prophet probability at a 1% false discovery rate was used as a cutoff value to generate SAINT-compatible input files. SAINT parameters were as follows: 5000 iterations, low mode Off (0), minFold 1 and normalization (1) (Choi et al, 2011). SAINT cutoff values of 0.75 were used to generate a high-confidence list of protein identifications.
2019-11-25 | PXD000381 | Pride
Project description:Using cDNA arrays, we compared G0 myoblasts (S48) with post-mitotic myotubes. Our findings define the transcriptional program of quiescent myoblasts in culture which show important similarities with muscle satellite cells, and establish that distinct gene expression profiles characterize irreversible and reversible arrest Cell were synchronized in G0 by resuspending them in semi-solid media for 48 hours and harvested for RNA isolation
2013-04-16 | E-GEOD-33676 | biostudies-arrayexpress
Project description:In this study, by using two classical macrophage cell models, RAW264.7 cell line from mouse and THP-1 cell line from human, combined with the applications of two classical stimulation methods for inducing classical activated (M1) and alternatively activated macrophages (M2) from the monocytes of both cell lines, we comprehensively identified and quantified proteins in different types of macrophages from both cell lines through high-throughput proteomics.
2021-06-18 | PXD019800 | Pride
Project description:Knockdown of MLL5 led to deregulation of S phase. To understand the molecular basis for this phenotype, we performed microarray analysis of S phase synchronized myoblasts. Genes differentially regulated by MLL5 knock down were revealed by microarray analysis using NIA15K mouse chips. Control and knock down cells were synchronized at G0 by suspension culture and reactivated to enter S phase by replating for 24hrs in growth medium.
2010-05-22 | E-GEOD-14931 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE22477: PHF8 mediates histone demethylation events in cell cycle progression [expression] GSE22478: PHF8 mediates histone demethylation events in cell cycle progression [ChIP-Seq] Refer to individual Series
2010-08-31 | E-GEOD-22400 | biostudies-arrayexpress