Journal: Multiple sclerosis (Houndmills, Basingstoke, England)

Article Title: Gene expression changes underlying cortical pathology: clues to understanding neurological disability in multiple sclerosis

doi: 10.1177/1352458513500554

Figure Lengend Snippet: Summary of gene profiling studies in grey matter tissue

Article Snippet: 6 MS (SP, PR, NA) 8 Ctl , Cerebral Cortex Frozen , Applied Biosystems Human Genome Survey Microarray v1.0 ~31,700 probes , Yes , Non-lesioned and lesioned cortex from MS brains was compared to control cortex. No genes were found to be significantly different between MS lesioned and non-lesioned cortex. Compared to controls, 532 genes were altered in MS cortex. Major findings of the study include increased mRNA levels of IgG-related genes, possibly due to meningeal plasma cells that are not infected by Epstein-Barr virus. , 26.

Techniques: Microarray, Infection

Journal: Nature Communications

Article Title: circNDUFB2 inhibits non-small cell lung cancer progression via destabilizing IGF2BPs and activating anti-tumor immunity

doi: 10.1038/s41467-020-20527-z

Figure Lengend Snippet: a A heatmap and volcano plot show 109 differentially expressed circRNAs in three paired samples of NSCLC by Arraystar Human Circular RNA Microarray. Cut off is Log 2 (fold change) > 1 or <−1.0, P value < 0.05. b Analysis for RNA levels of circNDUFB2 in additional 52 paired samples of NSCLC (left). Expression proportions of circNDUFB2 in histogram and pie chart (right). Log 2 (T/N expression) value > 1 as significantly higher expression, which <−1 as significantly lower expression, and between −1 and 1 as no significant change. N nontumorous tissue, T tumorous tissue. Data are presented as mean ± s.d. P values are calculated by paired two-sided t -test. n = 52 biologically independent paired tissues of NSCLC. c The backsplice junction site of circNDUFB2 was identified by Sanger sequencing. d PCR analysis for circNDUFB2 and β-actin in cDNA and genomic DNA. RH random hexamers, OdT oligo(dT) 18 primers, gDNA genomic DNA. Two independent experiments were carried out with similar results. e Analysis for RNA levels of circNDUFB2 and NDUFB2 after treatment with RNase R. n = 3 biologically independent samples. f Analysis for RNA abundance of circNDUFB2 and NDUFB2 treated with Actinomycin D (2 μg/ml) at the indicated time point. n = 3 biologically independent samples. g RNA levels of circNDUFB2 , NDUFB2 , β-actin , and U1 in the nuclear and cytoplasmic fractions of A549 and H1650 cells. n = 3 biologically independent samples. h RNA FISH analysis for circNDUFB2 in A549 cells, scale bar = 15 μm. Two independent experiments were carried out with similar results. Data are presented as mean ± s.d in e – g . P values are calculated by unpaired two-sided t -test in a , e – g .

Article Snippet: The labeled cRNAs were hybridized onto the Arraystar Human Circular RNA Microarray V1.0 (6x7K, Arraystar), which contains 5396 probes specific for human circular RNAs backsplice junction region.

Techniques: Microarray, Expressing, Sequencing

Journal: Frontiers in Immunology

Article Title: Applications of Protein Microarrays in Biomarker Discovery for Autoimmune Diseases

doi: 10.3389/fimmu.2021.645632

Figure Lengend Snippet: Major protein microarray platforms for biomarker discovery in autoimmune diseases.

Article Snippet: The HuProtTM Human Proteome Microarray V1.0 was designed by Zhu lab at Johns Hopkins School of Medicine and produced by CDI Laboratories around 2012, containing 16,368 recombinant GST-His-tagged human proteins expressed in S. cerevisiae , and the current v4.0 contains more than 21,000 unique proteins.

Techniques: Microarray, Biomarker Discovery, Protein Array, Recombinant, In Silico, Selection, In Situ, Peptide Microarray, Ab Array, Bioprocessing

Journal: Frontiers in Immunology

Article Title: Applications of Protein Microarrays in Biomarker Discovery for Autoimmune Diseases

doi: 10.3389/fimmu.2021.645632

Figure Lengend Snippet: Selective application of protein microarrays in biomarker discovery for autoimmune diseases.

Article Snippet: The HuProtTM Human Proteome Microarray V1.0 was designed by Zhu lab at Johns Hopkins School of Medicine and produced by CDI Laboratories around 2012, containing 16,368 recombinant GST-His-tagged human proteins expressed in S. cerevisiae , and the current v4.0 contains more than 21,000 unique proteins.

Techniques: Biomarker Discovery, Enzyme-linked Immunosorbent Assay, Western Blot, Microarray, Immunopeptidomics, Protein Array, Diagnostic Assay, Recombinant, Purification, Derivative Assay, Competitive ELISA, Peptide Microarray, Software, Construct, Bioprocessing, Ab Array, Clinical Proteomics, Expressing, Amplified Luminescent Proximity Homogenous Assay, Multiplex Assay, Glycoproteomics, Membrane, Sequencing, Immunofluorescence, Staining, Virus, Immunohistochemistry, cDNA Library Assay, Clone Assay, Suspension, Apoptosis Assay, Stripping Membranes, In Silico, Activity Assay, Cytokine Assay

Journal: American Journal of Respiratory and Critical Care Medicine

Article Title: A Network of Sputum MicroRNAs Is Associated with Neutrophilic Airway Inflammation in Asthma

doi: 10.1164/rccm.201912-2360OC

Figure Lengend Snippet: Weighted gene correlation network analysis of sputum microRNA expression and asthma features (n = 78 samples). Using expressed microRNAs (n = 221) in the sputum, six modules were identified. These modules had correlations with multiple demographic, clinical, physiologic, and sputum characteristics. Positive correlations are red, and negative correlations are blue. The microRNAs in the blue (nely) module were positively associated with age, asthma duration, hospitalizations in the previous year, bronchodilator response, and neutrophil and lymphocyte cell counts in the sputum; and negatively correlated with asthma quality of life (AQLQ), FEV1% predicted, and FVC% predicted at baseline. Values are correlation coefficient (nominal P value). BDR = bronchodilator response; Eos = eosinophil; FeNO = fractional exhaled nitric oxide; Lymph = lymphocyte; Mac = macrophage; miRNA = microRNA; Neu = neutrophil.

Article Snippet: RNA was labeled and hybridized to the Agilent Human microRNA (miRNA) Microarray v1.0 (Agilent Technologies).

Techniques: Expressing

Journal: American Journal of Respiratory and Critical Care Medicine

Article Title: A Network of Sputum MicroRNAs Is Associated with Neutrophilic Airway Inflammation in Asthma

doi: 10.1164/rccm.201912-2360OC

Figure Lengend Snippet: Weighted gene correlation network analysis of microRNA (miR) and mRNA expression in matched sputum samples (n = 21). Weighted gene correlation network analysis heatmap of the correlation between genes expressed in the sputum (n = 16,966). This analysis identified 32 gene modules correlated with the 12 microRNAs included in the nely microRNA module in paired mRNA and microRNA samples obtained from the same individuals. Positive correlations are red, and negative correlations are blue. Two modules had the most positive and negative correlations. The lightcyan mRNA module had positive correlations with 10 nely module microRNAs, and the turquoise module had negative correlations with 8 nely module microRNAs. Gene enrichment analysis of the lightcyan mRNA module revealed enrichment for TLR (Toll-like receptor) pathways and T-helper cell type 17 pathways, and the turquoise mRNA module was enriched for the unfolded protein response (UPR). These putative biological functions for the two modules are highlighted in the module. Values are correlation coefficient (nominal P value).

Article Snippet: RNA was labeled and hybridized to the Agilent Human microRNA (miRNA) Microarray v1.0 (Agilent Technologies).

Techniques: Expressing

Journal: International Journal of Molecular Sciences

Article Title: Autophagy in Premature Senescent Cells Is Activated via AMPK Pathway

doi: 10.3390/ijms13033563

Figure Lengend Snippet: AMPK activation is linked to the increase of AMP/ATP ratio in senescent cells. ( A ) ATP and AMP levels in senescent and young cells were quantified by reverse-phase HPLC. Data represented as mean ± S.D. of three independent determinations. * indicated a significant difference at the level of P < 0.05, ** indicated a significant difference at the level of P < 0.01. ( B ) Upper panel: changes of the expression of three energy production-related genes, PDK4, PFKP and FH were analyzed with microarray in senescent cells. Lower panel: change of the expression of the three genes was confirmed by real-time PCR. Data represented as mean ± SD of three independent experiments. Y: young cells; S: senescent cells. ** indicated a significant difference at the level of P < 0.01.

Article Snippet: The product No. of gene chip used was 220,010, Jingxin human whole genome oligonucleotide microarray V1.0 with 22,000 probes.

Techniques: Activation Assay, Expressing, Microarray, Real-time Polymerase Chain Reaction