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Project description:RNA Sequencing analysis of melanomas isolated from TN GEM models
| PRJNA812496 | ENA
Project description:Tn antigen (Tn), a single N-acetylgalactosamine (GalNAc) monosaccharide attached to protein Ser and Thr residues, is found on most solid tumors yet rarely detected in adult tissues: featuring it one of the most distinctive signatures of cancers. Although it is prevalent in cancers, Tn-glycosylation sites are not entirely clear owing to the lack of suitable technology. Knowing the Tn-glycosylation sites will spur the development of the new vaccines, diagnostics, and therapeutics of cancers. Here, we report a novel technology named EXoO-Tn for large-scale mapping of Tn-glycosylation sites. EXoO-Tn utilizes glycosyltransferase C1GalT1 and isotopically-labeled UDP-Gal(13C6) to tag and convert Tn to Gal(13C6)-Tn. This exquisite Gal(13C6)-Tn structure is recognized by a human-gut-bacterial enzyme, called OpeRATOR, that specifically cleaves N-termini of the Gal(13C6)-Tn-occupied Ser and Thr residues to yield site-containing glycopeptides. The enzymes C1GalT1 and OpeRATOR could be used concurrently in one-pot. The effectiveness of EXoO-Tn was evaluated by analyzing Jurkat cells, where 947 Tn-glycosylation sites from 480 glycoproteins were mapped. Bioinformatic analysis of the identified site-specific Tn-glycoproteins revealed conserved motif, cellular localization, relative position in proteins, and mapped site-specific Tn-glycoproteome in different studies. Given the significance of Tn in cancers, EXoO-Tn is anticipated to have broad utilities in clinical study of cancers.
2022-02-15 | PXD014390 | Pride
Project description:Background: Histone deacetylase (HDAC) is strongly associated with epigenetic regulation and carcinogenesis, and its inhibitors induce the differentiation or apoptosis of cancer cells. Valproic acid (VPA) is one of the clinically available HDAC inhibitors. We investigated the anticancer effects of VPA in combination with gemcitabine (GEM) in cholangiocarcinoma cell line, and explored the mechanisms of the anticancer effects using microarray analysis. Methods: A human cholangiocarcinoma cell line (HuCCT1) was used. The anticancer effects of VPA, or gemcitabine (GEM), and the effects of VPA combined with GEM, were studied by cell proliferation assay. The microarray analysis was performed, the genes were picked up using Gene Spring GX11.5, Ingenuity Pathways Analysis (IPA) was performed, and then the gene-expression was determined by RT-PCR. Results: GEM (5nM) and VPA (0.5mM) reduced by 23%, which significantly augmented the anticancer effect of GEM alone or VPA alone (P<0.01). Using the microarray analysis, forty-three genes were identified with the comparison between GEM group and GEM plus VPA combination group. The interactions were shown between genes of the “Cellular Development” relevant to the differentiation of cancer cell using IPA.
2011-02-09 | GSE27036 | GEO
Project description:Light dependent gene expression in D. shibae wildtype compared to the gene expression in the transposonmutants D. shibae Dshi_1135::Tn, D. shibae ppaA::Tn and D. shibae ppsR::Tn. Dinoroseobacter shibae DFL12T (DSM 16493T) and the transposonmutants D. shibae Dshi_1135::Tn, D. shibae ppaA::Tn and D. shibae ppsR::Tn were grown in artificial saltwater minimal medium (SWM) in baffled flasks shaking at 180 rpm and 30 °C and incubation was performed under light, dark and bluelight conditions. D. shibae wild type and mutant strain were grown under aerobic conditions up to the mid exponential growth phase (OD578 nM 0.5).
2023-10-01 | GSE244289 | GEO
Project description:Background: Histone deacetylase (HDAC) is strongly associated with epigenetic regulation and carcinogenesis, and its inhibitors induce the differentiation or apoptosis of cancer cells. Valproic acid (VPA) is one of the clinically available HDAC inhibitors. We investigated the anticancer effects of VPA in combination with gemcitabine (GEM) in cholangiocarcinoma cell line, and explored the mechanisms of the anticancer effects using microarray analysis. Methods: A human cholangiocarcinoma cell line (HuCCT1) was used. The anticancer effects of VPA, or gemcitabine (GEM), and the effects of VPA combined with GEM, were studied by cell proliferation assay. The microarray analysis was performed, the genes were picked up using Gene Spring GX11.5, Ingenuity Pathways Analysis (IPA) was performed, and then the gene-expression was determined by RT-PCR. Results: GEM (5nM) and VPA (0.5mM) reduced by 23%, which significantly augmented the anticancer effect of GEM alone or VPA alone (P<0.01). Using the microarray analysis, forty-three genes were identified with the comparison between GEM group and GEM plus VPA combination group. The interactions were shown between genes of the “Cellular Development” relevant to the differentiation of cancer cell using IPA. Total RNA was isolated from both the stimulated and unstimulated cells (HuCCT-1) using RNeasy Mini kit (Qiagen, Valencia, CA). Relative purity was examined using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). RNA expression was analyzed using GeneChip○R Human Gene 1.0 ST Array (Affymetrix, Santa Clara, CA, USA), containing 28,869 oligonucleotide probes for known and unknown genes. First standard cDNA was synthesized from 300 ng of total RNA by using GeneChip○R Whole Transcript (WT) cDNA Synthesis and Amplification Kit (Affymetrix) according to the manufacturer’s instructions. 10 μg of cRNA were input into the second-cycle cDNA reaction. cDNA was fragmented and end-labeled with the GeneChip○R WT Terminal Labeling Kit (Affymetrix). Approximately 5.5μg of fragmented and labeled DNA target was hybridized to the Affymetrix GeneChip○R Human Gene 1.0 ST Array at 45°C for 17h on a GeneChip○R Hybridization Oven 640 (Affymetrix) according to the manufacturer’s recommendation. Hybridized arrays were washed and stained on a GeneChip○R Fluidics Station 450 and scanned on a GeneChip○R Scanner 3000 7G (Affymetrix), and then generated CEL files for each array. The microarray data was normalized by GeneSpring GX 11.5 software (Agilent). The cut-off value was set at 0.5 to 2.0 for the ratio (more than 2.0: up-regulation, 0.5-2.0: no change, less than 0.5: down-regulation). Gene Ontology (GO) was analyzed using GeneSpring GX 11.5 software (Agilent), and p-value < 0.05 was used for significance. Then we used Ingenuity Pathway Analysis (IPA) 8.7 (http://www.ingenuity.com) to determine the functional pathways associated with the set of differentially expressed genes between genotypes. IPA utilizes the knowledge in the literature about biological interactions among genes and proteins.
2011-02-09 | E-GEOD-27036 | biostudies-arrayexpress
Project description:The goal of this Tn-Seq study was to determine important determinants of Acinetobacter baumannii tolerance of sub-MIC concentrations of benzalkonium chloride. This Tn-seq data was then utilized to aide in the determination of the sub-MIC mechanism of action for benzalkonium chloride.
2018-01-23 | GSE96745 | GEO
Project description:au14-01_tn - Observation of the effects of the product Tn on the expression of genes of A. thaliana. - Observation of the effects of the product Tn on the expression of genes of Arabidopsis thaliana related to nutrition and development. - Each plant is sprayed with a product. 24h or 48h after treatment, a leaf is removed for RNA extraction and analysis.
2017-02-01 | GSE93095 | GEO