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Biotechnology Information gene expression microarray experiments
Gene Expression Microarray Experiments, supplied by Biotechnology Information, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Article Title: Integrated Network Analysis Identifies Fight-Club Nodes as a Class of Hubs Encompassing Key Putative Switch Genes That Induce Major Transcriptome Reprogramming during Grapevine Development
Article Snippet: Accession Numbers The grapevine berry RNA-Seq data are MIAME compliant and have been deposited in a MIAME-compliant database (Gene Expression Omnibus [ http://www.ncbi.nlm.nih.gov/geo/ ] accession number {"type":"entrez-geo","attrs":{"text":"GSE62744","term_id":"62744"}} GSE62744 ) at the National Center for Biotechnology Information.

Article Title: Transcription and FACT facilitate the restoration of replication-coupled chromatin assembly defects.
Article Snippet: Raw data from MNase-seq have been deposited at the MIAME-compliant Gene Expression Omnibus (GEO) database at the National Center for Biotechnology Information (http:// www. ncbi. nlm. nih. gov/ geo/), and are accessible through the accession number GSE228861.

Article Title: Transcription and FACT facilitate the restoration of replication-coupled chromatin assembly defects
Article Snippet: Raw data from MNase-seq have been deposited at the MIAME-compliant Gene Expression Omnibus (GEO) database at the National Center for Biotechnology Information ( http://www.ncbi.nlm.nih.gov/geo/ ), and are accessible through the accession number GSE228861.

Article Title: Unraveling the key molecular events of Pinot noir berry ripening under varying crop load
Article Snippet: Data availability The grapevine berry RNA-Seq data are MIAME compliant and have been deposited in a MIAME-compliant database (Gene Expression Omnibus) at the National Center for Biotechnology Information: control samples can be found under the accession number GSE98923 (Fasoli et al., 2018), whereas cluster thinning related samples under GSE101532.

Microarray:

Article Title: A Vitamin D-RelB/NF-κB Pathway Limits Chandipura Virus Multiplication by Rewiring the Homeostatic State of Autoregulatory Type 1 IFN-IRF7 Signaling.
Article Snippet: .. The Minimum Information About a Microarray Experiment version of our microarray data is available at National Center of Biotechnology Information Gene Expression Omnibus under accession number GSE176446 (https://www.ncbi.nlm. nih.gov/geo/query/acc.cgi). .. For investigating the vitamin D activated gene program, we examined a previously published transcriptomics data set obtained using the THP1 human-derived monocytic cell line (National Center of Biotechnology Information Gene Expression Omnibus, accession number GSE57028) (32).

Article Title: DUSP8 Regulates Cardiac Ventricular Remodeling by Altering ERK1/2 Signaling
Article Snippet: Once the online version of the published article for which permission is being requested is located, click can be obtained via RightsLink, a service of the Copyright Clearance Center, not the EditorialCirculation Research Requests for permissions to reproduce figures, tables, or portions of articles originally published inPermissions: at University College London (ucl) / England on May 31, 2016http://circres.ahajournals.org/Downloaded from Online Figures and Online Tables for: DUSP8 regulates cardiac ventricular remodeling by altering ERK1/2 signaling Ruijie Liu, Jop H. van Berlo, Allen J. York, Marjorie Maillet, Ronald J. Vagnozzi, Jeffery D. Molkentin Online Figure I. Dusp8 mRNA is highly expressed in human dilated cardiomyopathy patients. .. Data in the National Center for Biotechnology Information Gene Expression Omnibus (NCBI GEO) database contained an elaborate microarray experiment from human heart biopsies (GEO accession GDS2206, reference #32) that showed an increase in Dusp8 mRNA in patients with dilated cardiomyopathy (DCM). ..

Article Title: Cerebellin 4, a synaptic protein, enhances inhibitory activity and resistance of neurons to amyloid-β toxicity.
Article Snippet: Imbalances between excitatory and inhibitory transmissions in the brain anticipate the neuronal damage and death that occur in the neurodegenerative diseases like Alzheimer’s disease (AD).. We previously showed that amyloid-b (Aß), a natural peptide involved in the onset and development of AD, counteracts the neurotrophic activity of the nerve growth factor (NGF) by dampening the g-aminobutyric acid (GABA)ergic connectivity of cultured hippocampal neurons.. Neuronal plasticity is partly controlled by the NGF-promoted expression of the homologue of enhancer-of-split 1 (Hes1), a transcription factor that regulates the formation of GABAergic synapses.

Gene Expression:

Article Title: A Vitamin D-RelB/NF-κB Pathway Limits Chandipura Virus Multiplication by Rewiring the Homeostatic State of Autoregulatory Type 1 IFN-IRF7 Signaling.
Article Snippet: .. The Minimum Information About a Microarray Experiment version of our microarray data is available at National Center of Biotechnology Information Gene Expression Omnibus under accession number GSE176446 (https://www.ncbi.nlm. nih.gov/geo/query/acc.cgi). .. For investigating the vitamin D activated gene program, we examined a previously published transcriptomics data set obtained using the THP1 human-derived monocytic cell line (National Center of Biotechnology Information Gene Expression Omnibus, accession number GSE57028) (32).

Article Title: DUSP8 Regulates Cardiac Ventricular Remodeling by Altering ERK1/2 Signaling
Article Snippet: Once the online version of the published article for which permission is being requested is located, click can be obtained via RightsLink, a service of the Copyright Clearance Center, not the EditorialCirculation Research Requests for permissions to reproduce figures, tables, or portions of articles originally published inPermissions: at University College London (ucl) / England on May 31, 2016http://circres.ahajournals.org/Downloaded from Online Figures and Online Tables for: DUSP8 regulates cardiac ventricular remodeling by altering ERK1/2 signaling Ruijie Liu, Jop H. van Berlo, Allen J. York, Marjorie Maillet, Ronald J. Vagnozzi, Jeffery D. Molkentin Online Figure I. Dusp8 mRNA is highly expressed in human dilated cardiomyopathy patients. .. Data in the National Center for Biotechnology Information Gene Expression Omnibus (NCBI GEO) database contained an elaborate microarray experiment from human heart biopsies (GEO accession GDS2206, reference #32) that showed an increase in Dusp8 mRNA in patients with dilated cardiomyopathy (DCM). ..

Article Title: Cerebellin 4, a synaptic protein, enhances inhibitory activity and resistance of neurons to amyloid-β toxicity.
Article Snippet: Imbalances between excitatory and inhibitory transmissions in the brain anticipate the neuronal damage and death that occur in the neurodegenerative diseases like Alzheimer’s disease (AD).. We previously showed that amyloid-b (Aß), a natural peptide involved in the onset and development of AD, counteracts the neurotrophic activity of the nerve growth factor (NGF) by dampening the g-aminobutyric acid (GABA)ergic connectivity of cultured hippocampal neurons.. Neuronal plasticity is partly controlled by the NGF-promoted expression of the homologue of enhancer-of-split 1 (Hes1), a transcription factor that regulates the formation of GABAergic synapses.

Article Title: miRNAs regulate acute transcriptional changes in broiler embryos in response to modification of incubation temperature
Article Snippet: Raw probe signal intensity was pre-processed and normalized using Perfect Matched and Detection Above Background features of Affymetrix Expression Consol software. .. Data were submitted to the MIAME-compliant database Gene Expression Omnibus (accession number: GSE83703-GSE83704) accessible via the National Center for Biotechnology Information ( www.ncbi.nlm.nih.gov/geo ). .. Differential expression of miRNAs was computed by analysis of variance (JMP Genomics, SAS-Institute, Cary, NC, USA).



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ABCG2 upregulation is associated with SIK3 attenuation. (A) List of ABC family proteins from <t>microarray</t> data for which the expression changed more than 1.5-fold compared with control cells. (B) The mRNA expression levels of ABC proteins were verified by real-time PCR in OVCAR4 and SKOV3 cells. The white bar (shLuc) represents control cells, and the gray bar (shSIK3#01) and black bar (shSIK3#61) represent indicated cells with SIK3 knockdown. Data are represented as the mean ± SEM from three independent experiments and analyzed by one-way ANOVA. *: p <0.05 and **: p <0.01 (compared to the shLuc control). Note that ABCG1 and ABCG2 were both significantly upregulated in cells with SIK3 knocked down by shSIK3#01 and shSIK3#61. (C) The protein expression levels of ABCG1 and ABCG2 were further verified by Western blotting. Note that only ABCG2 was upregulated in OVCAR4 and SKOV3 cells with SIK3 knocked down by shSIK3#01 and shSIK3#61. (D) The functional MDR activity of the ABCG2 protein was determined using an MDR assay kit (Abcam). A total of 2 x 10 5 suspended cells were pretreated with the inhibitor novobiocin (50 nM) or DMSO. Then, diluted Efflux Gold Detection Reagent was added at 37°C for 30 minutes. The cellular orange fluorescence signal of the Efflux Gold Detection Reagent was measured immediately by flow cytometry in the living (PI-negative) cell population. The numbers in the upper left corners are MAF values.
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ZEB1-AS1 sponges miR-141-3p in CRC cells. ( A ) Nuclear and cytoplasmic fractionation was analyzed for ZEB1-AS1 expression in SW480 and LOVO. ( B ) The microRNA array analysis in normal and tumor tissues. ( C ) The potential binding sites between ZEB1-AS1 and miR-141-3p. ( D ) The expressions of miR-141-3p in CRC tissues were detected by RT-qPCR. ( E ) Luciferase reporter assay showed ZEB1-AS1-wt activity was impaired by miR-141-3p. ( F ) The expression of miR-141-3p in SW480 and LOVO was upregulated after ZEB1-AS1 expression was downregulated identified by RT-qPCR. ( G ) The expression of miR-141-3p was negatively correlated with ZEB1-AS1 expression in CRC tissues. * P < 0.05.

Journal: International Journal of Medical Sciences

Article Title: Long noncoding RNA ZEB1-AS1 acts as a Sponge of miR-141-3p to Inhibit Cell Proliferation in Colorectal Cancer

doi: 10.7150/ijms.46698

Figure Lengend Snippet: ZEB1-AS1 sponges miR-141-3p in CRC cells. ( A ) Nuclear and cytoplasmic fractionation was analyzed for ZEB1-AS1 expression in SW480 and LOVO. ( B ) The microRNA array analysis in normal and tumor tissues. ( C ) The potential binding sites between ZEB1-AS1 and miR-141-3p. ( D ) The expressions of miR-141-3p in CRC tissues were detected by RT-qPCR. ( E ) Luciferase reporter assay showed ZEB1-AS1-wt activity was impaired by miR-141-3p. ( F ) The expression of miR-141-3p in SW480 and LOVO was upregulated after ZEB1-AS1 expression was downregulated identified by RT-qPCR. ( G ) The expression of miR-141-3p was negatively correlated with ZEB1-AS1 expression in CRC tissues. * P < 0.05.

Article Snippet: Shanghai Biotechnology Co., Ltd conducted the microRNA microarray gene expression experiments and data analysis.

Techniques: Fractionation, Expressing, Binding Assay, Quantitative RT-PCR, Luciferase, Reporter Assay, Activity Assay

ABCG2 upregulation is associated with SIK3 attenuation. (A) List of ABC family proteins from microarray data for which the expression changed more than 1.5-fold compared with control cells. (B) The mRNA expression levels of ABC proteins were verified by real-time PCR in OVCAR4 and SKOV3 cells. The white bar (shLuc) represents control cells, and the gray bar (shSIK3#01) and black bar (shSIK3#61) represent indicated cells with SIK3 knockdown. Data are represented as the mean ± SEM from three independent experiments and analyzed by one-way ANOVA. *: p <0.05 and **: p <0.01 (compared to the shLuc control). Note that ABCG1 and ABCG2 were both significantly upregulated in cells with SIK3 knocked down by shSIK3#01 and shSIK3#61. (C) The protein expression levels of ABCG1 and ABCG2 were further verified by Western blotting. Note that only ABCG2 was upregulated in OVCAR4 and SKOV3 cells with SIK3 knocked down by shSIK3#01 and shSIK3#61. (D) The functional MDR activity of the ABCG2 protein was determined using an MDR assay kit (Abcam). A total of 2 x 10 5 suspended cells were pretreated with the inhibitor novobiocin (50 nM) or DMSO. Then, diluted Efflux Gold Detection Reagent was added at 37°C for 30 minutes. The cellular orange fluorescence signal of the Efflux Gold Detection Reagent was measured immediately by flow cytometry in the living (PI-negative) cell population. The numbers in the upper left corners are MAF values.

Journal: Journal of Cancer

Article Title: Downregulated Salt-inducible Kinase 3 Expression Promotes Chemoresistance in Serous Ovarian Cancer via the ATP‐binding Cassette Protein ABCG2

doi: 10.7150/jca.34886

Figure Lengend Snippet: ABCG2 upregulation is associated with SIK3 attenuation. (A) List of ABC family proteins from microarray data for which the expression changed more than 1.5-fold compared with control cells. (B) The mRNA expression levels of ABC proteins were verified by real-time PCR in OVCAR4 and SKOV3 cells. The white bar (shLuc) represents control cells, and the gray bar (shSIK3#01) and black bar (shSIK3#61) represent indicated cells with SIK3 knockdown. Data are represented as the mean ± SEM from three independent experiments and analyzed by one-way ANOVA. *: p <0.05 and **: p <0.01 (compared to the shLuc control). Note that ABCG1 and ABCG2 were both significantly upregulated in cells with SIK3 knocked down by shSIK3#01 and shSIK3#61. (C) The protein expression levels of ABCG1 and ABCG2 were further verified by Western blotting. Note that only ABCG2 was upregulated in OVCAR4 and SKOV3 cells with SIK3 knocked down by shSIK3#01 and shSIK3#61. (D) The functional MDR activity of the ABCG2 protein was determined using an MDR assay kit (Abcam). A total of 2 x 10 5 suspended cells were pretreated with the inhibitor novobiocin (50 nM) or DMSO. Then, diluted Efflux Gold Detection Reagent was added at 37°C for 30 minutes. The cellular orange fluorescence signal of the Efflux Gold Detection Reagent was measured immediately by flow cytometry in the living (PI-negative) cell population. The numbers in the upper left corners are MAF values.

Article Snippet: TRIzol-isolated RNA samples were shipped on dry ice to Welgene Biotech (Taiwan), where the gene expression microarray experiments were performed as a contract service.

Techniques: Microarray, Expressing, Control, Real-time Polymerase Chain Reaction, Knockdown, Western Blot, Functional Assay, Activity Assay, Fluorescence, Flow Cytometry