Proteomic of sacha inchi husk extract treatment on colorectal cancer cell
Ontology highlight
ABSTRACT:
INSTRUMENT(S):
ORGANISM(S): Homo Sapiens (human)
TISSUE(S): Cell Culture
SUBMITTER: 
Supawadee Osotprasit
LAB HEAD: Supawadee Osotprasit
PROVIDER: PXD061526 | Pride | 2025-11-07
REPOSITORIES: Pride
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| HCT1.mgf | Mgf | |||
| HCT1.mzML | Mzml | |||
| HCT1.timeseries.data | Other | |||
| HCT1_peptides_1_1_0.mzid | Mzid | |||
| HCT2.mgf | Mgf |
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Project description:Proteomic analyses were conducted, providing insights into molecular changes in proteins. Functional annotation of significant up/down-regulated proteins supported the reduction of cancer cell activities.
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Project description:Euglena gracilis is a unicellular freshwater flagellate, which uses the gravitational vector for orientation in the water column in the dark. This allows the cell to reach areas in the water column for reproduction and growth. How exactly the gravitational vector is perceived, and which intracellular pathways are involved in the signaling is not very well understood so far. In the past, parabolic flight campaigns were used to study the swimming behavior of Euglena gracilis under altered gravitational accelerations. It was shown that cells adapt their swimming direction very fast: in the dark under 1xg cell show negative gravitaxis, i.e. they move upwards in the water column of the experiment hardware and against the gravitational vector. With onset of the first hypergravity period of 1.8xg the precision of upward swimming increases slightly. This first hyper gravity lasts for only 20 seconds and is followed by 22 sec of microgravity. During this period no gravitational vector is perceived by the cells, therefore they lack a cue for orientation and move randomly in all direction. In the subsequent hyper gravity period of 1.8xg, which also lasts for 20 sec, cells direct their movement again and swim upwards. Over different parabolic flight campaigns and other experiments it was shown that this gravitactic behavior is linked to changes in membrane potential, calcium and cAMP concentration. However, due to the lack of genomic and transcriptomic data, it was so far not possible to link the differential movement to the abundance of distinct mRNA transcripts. In contrast, other model organisms, such as Arabidopsis thaliana, have been analyzed by means of gene expression with respect to the effects of altered gravitational accelerations. Also various human cell lines have shown to adapt their gene expression in dependence of the prevailing acceleration. With the recently published Euglena gracilis transcriptome, we now aimed at analyzing effects of altered acceleration on the gene expression in the flagellate. Therefore, Euglena gracilis samples were taken in the course of the 29th DLR parabolic flight campaign during parabola 1 and 31 (time difference of 2 hours and 30 additional parabolas). During both parabolas samples were fixed with TRIzol at 1xg just before onset of the first hyper gravity period, 20 sec into hyper gravity (1.8xg), 20 sec into microgravity (µg) and 20 sec into the last hypergravity period.
2019-07-09 | E-MTAB-8064 | biostudies-arrayexpress
Project description:Supplement S1: Figure S1. (a) Effect of culture age of Euglena gracilis on gene expression, determined with gene arrays analysis. Total number of differentially expressed genes classified into groups of fold-change-ranges in Euglena gracilis cells of different culture age (5 d, 9 d, 11 d) compared to culture age of six days. Underlying data are presented under the figure or in “FC in classes”, respectively. The total number of investigated genes on microarray was n = 20296. Data were retrieved from four independent cell cultures. (b) Effect of culture age of Euglena gracilis on gene expression. Fraction of differentially expressed genes in percent of all investigated transcripts [n = 20,396] classified into groups of fold-change-ranges in Euglena gracilis cells of different culture age (5 d, 9 d, 11 d) compared to culture age of six days. Underlying data are presented under the figure or in “FC in classes”, respectively. For more details, please see the legend Figure S1 a. (c) Effect of culture age of Euglena gracilis on gene expression. Fraction differentially expressed genes (DEGs) above (“upregulation”), below (“downregulation”) or above AND below (“all”), respectively a certain threshold (th). In contrast to (b), where the fold changes are provided in classes, all DEGs above, below, or above AND below as certain threshold are summarized. In addition, Supplement S1 contains all raw data about all DEGs detected and a rankling of the genes regarding their fold changes (FCs). Supplement S2: Determination of differential gene expression with respect to culture age in Euglena gracilis, obtained with micro-arrays. The table “Overlapping DEGs” contains all transcripts, which were found to be differentially expressed in Euglena gracilis at all three investigated days of culture age (5, 9, or 11 days, respectively), against the 6-day samples. In the table “Overlapping DEGs ranked”, the data are ranked according to their fold change. Supplement S3: Transcription of Euglena gracilis cells of different culture age (5, 9, and 11 d, respectively) was compared with the transcription of cells after 6 days of culturing. All data were obtained in quadruplicate. This supplementary data show the possible functions of the proteins encoded by the DEGs (differentially expressed genes), which were differentially expressed for the corresponding days. Table “Diff transcripts funct.” gives a general overview about gene expression changes for all days. The other tables list the possible function of the DEGs for each particular day. The lists only contain genes where a function could be assigned. Complete lists of DEGs also including transcripts with unknown function are provided in Supplement S1. Supplement S4: Determination of gene expression changes with respect to culture age in Euglena gracilis samples of cells were analyzed after 5 d, 9 d, and 11 days of growth in batch cultures, and their gene expression was compared with the gene expression of cells with a culture age of 5 d. For each day, the number of differentially expressed genes (DEGs) each showing the same GO terms were summed up. In order to correlate these changes with the number of all genes with the same GO term in Euglena gracilis, data from sequencing projects were employed [1,2]. Genes with the same GO terms were counted and correlated with the number of observed DEGs in Euglena gracilis. In the first table, GO terms of DEGs were assigned to corresponding days of culturing and correlated with the data of [1, 2] (total numbers and ratios). Diagram “Ratio of DEGs compared to Cordoba et al. [%]” visualizes the ratio of DEGs with total data of [7]. The second diagram shows the number of GO terms of DEGs, which were found at day 9 AND day 11. The change between the two days is provided. Data are visualized in the diagram “Fraction of DEGs of a certain GO over time”. Ref. [2]: Additional file 2: Table S1 “proteome”. Ref. [1]: Supplementary Data, Table S2. Supplement S5: Amino acid sequences of proteins, which were found to become differentially expressed with respect to culture age of Euglena gracilis cultures. [1] Cordoba, J.; Perez, E.; Van Vlierberghe, M.; Bertrand, A.R.; Lupo, V.; Cardol, P.; Baurain, D. De novo transcriptome meta-assembly of the mixotrophic freshwater microalga Euglena gracilis. Genes 2021, 12, 842. https://doi.org/10.3390/genes12060842. [2] Ebenezer, T.E.; Zoltner, M.; Burrell, A.; Nenarokova, A.; Novák Vanclová, A.M.G.; Prasad, B.; Soukal, P.; Santana-Molina, C.; O’Neill, E.; Nankissoor, N.N.; et al. Transcriptome, proteome and draft genome of Euglena gracilis. BMC Biol. 2019, 17, 11. https://doi.org/10.1186/s12915-019-0626-8.
2024-04-01 | E-MTAB-13906 | biostudies-arrayexpress
Project description:Purpose: Investigate effects of high salt on human macrophage activation Methods: Human monocytes-derived macrophages were treated by additional 51mM NaCl for 24 hours (NaCl groups) or not (Control groups). mRNA profiles were generated by RNA-Seq, in triplicate, using Ion proton（Life tech). qRT–PCR validation was performed using SYBR Green assays. Results: High salt significantly promotes pro-inflammatory gene expressions,while suppresses the expressions of anti-inflammatory genes and pro-endocytic genes in human macrophages. Conclusions: Our results identify a novel macrophage activation state, M(Na), and high salt as a potential environmental risk factor for lung inflammation through the induction of M(Na) Human monocytes-derived macrophages were treated by additional 51mM NaCl for 24 hours (NaCl groups) or not (Control groups). mRNA profiles were generated by RNA-Seq, in triplicate, using Ion proton（Life tech). qRT–PCR validation was performed using SYBR Green assays.
2015-09-23 | E-GEOD-68482 | biostudies-arrayexpress
Project description:DEAD-box ATPases belong to an abundant class of proteins that are involved in virtually all aspects of RNA metabolism and are found in all kingdoms of life. When bound to a DEAD-box ATPase, the RNA substrate is forced into a kinked conformation that is incompatible with helical structures. Distortion of the RNA can result in unwinding of short RNA duplexes (helicase activity) or destabilize RNA-protein interactions, allowing DEAD-box ATPases to remodel mRNPs (RNPase activity). The RNPase activity makes DEAD-box ATPases suitable molecular building blocks for the implementation of checkpoints that confer directionality to the process of RNA biogenesis. Here, we provide data that characterizes the DEAD-box ATPase Dbp2 (SPBP8B7.16c) of the fission yeast Schizosaccharomyces pombe. Using calibrated RNAPII-ChIP-seq, we determined the transcription profiles of a conditional depletion strain of Dbp2 and the corresponding wild type. For this, we placed the endogenous dbp2 gene under the control of the P.nmt1 promoter, which is repressed in the presence of thiamine. Cells were crosslinked at the beginning (t0) or the end (t9) of a 9h shift to thiamine-containing YES medium. S. cerevisiae spike-in cells were added in a 1:5 OD600 ratio immediately before crosslinking.
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Project description:Acidification of seawater due to anthropogenic CO2, called as ocean acidification (OA), makes most coastal environments unfavorable for oysters. This is a serious socio-economical issue for China which is accounting for >70% of the world’s edible oyster supply. Understanding of OA effects at proteome level could lead to a better aquaculture management. Here, we present an iTRAQ based protein profiling analysis for the detection and quantification of proteome change under OA in one of the early life stages of a commercially important oyster species, Crassostrea hongkongensis. The completion of the genome sequence for oysters enabled us to confidently quantify over 1500 proteins in the larval oyster. Over 10% of proteome was altered in response to OA process at pH 7.6. Analysis of differentially expressed proteins and their associated pathways indicated that up-regulation of calcification, metabolic processes, cytoskeletal functions, oxidative stress and cell signaling processes might have been used by larvae to acclimate under OA. Although the expressions of cytoskeletal and signal transduction proteins were down-regulated in response to OA, there was no marked alternation in developmental processes such as metamorphic success. This study suggests that the estuarine edible oyster possess an adequate short-term adaptability or acclimation mechanism at proteome level to tolerate near-future OA scenario.
2015-10-29 | PXD002138 | Pride
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