Journal: International Journal of Chronic Obstructive Pulmonary Disease

Article Title: Identifying targets for COPD treatment through gene expression analyses

doi:

Figure Lengend Snippet: Summary of gene expression profiling studies involving human COPD/emphysema samples

Article Snippet: COPD GOLD2 vs. GOLD0 , Whole lung , Incyte Unigem high-density microarray (10,000 transcripts) SAGE (59,000 tags) , Apoptosis-related genes Inflammation-related genes Transcription factors (increased) Collagens (decreased) , Egr-1/Fos CTGF, CYR61, CX3CL1, TGFB1, and PDGFRA , .

Techniques: Expressing, Functional Assay, Microarray

Journal: Experimental eye research

Article Title: A novel electro-chemotactic approach to impact the directional migration of transplantable retinal progenitor cells

doi: 10.1016/j.exer.2019.06.002

Figure Lengend Snippet: Primers used for reverse transcription-polymerase chain reaction of retinal progenitor Cells (RPCs).

Article Snippet: The relative change in expression levels for each product between the unstimulated and experimental conditions was represented as 2 −∆∆Ct ( Thakur, Mishra et al. 2018 ). table ft1 table-wrap mode="anchored" t5 Table 1. caption a7 GENE ASSAY ID UniGene GenBank Size (Base pair) GAPDH Mm99999915 Mm.304088 {"type":"entrez-nucleotide","attrs":{"text":"NM_001289726.1","term_id":"576080554","term_text":"NM_001289726.1"}} NM_001289726.1 107 CXCR4 Mm01996749 Mm.1401 {"type":"entrez-nucleotide","attrs":{"text":"NM_009911.3","term_id":"116268122","term_text":"NM_009911.3"}} NM_009911.3 105 Open in a separate window Primers used for reverse transcription-polymerase chain reaction of retinal progenitor Cells (RPCs).

Techniques: Reverse Transcription Polymerase Chain Reaction

Journal: Genome Biology

Article Title: Folliculin-interacting protein FNIP2 impacts on overweight and obesity through a polymorphism in a conserved 3′ untranslated region

doi: 10.1186/s13059-022-02798-5

Figure Lengend Snippet: Multifactorial genetic model for overweight and obesity risk. A Multifactorial model to predict body mass index (BMI). Estimated parameters and 95% CI, plus p -values of variables in the multifactorial model. The linear regression model included the rs2291007 SNP (in additive form), three gene expression variables ( FNIP2 , FNIP1 , and FLCN ), plus sex, age, and the interaction between FNIP2 gene expression and rs2291007. B Bootstrap validation of the multifactorial model. Multifactorial model was validated through bootstrap validation, using 2000 bootstrap samples, which correction by optimism (MSE, Mean Square Error). C Variable importance plot for the multifactorial model, using χ 2 – df (degrees of freedom) as metrics for the importance of each variable

Article Snippet: RT-PCR reactions were performed as previously described [ ] using QuantStudio 12 K Flex Real-Time PCR System (Life Technologies Inc., Carlsbad, CA, USA), with specific Taqman probes: FNIP2 (Hs01574322_m1), FLCN (Hs00376065_m1), FNIP1 (Hs00382846_m1), GAPDH (Hs02786624_g1).

Techniques: Gene Expression, Biomarker Discovery

Journal: Insects

Article Title: Temporal miRNA Biomarkers for Pupal Age Estimation in Sarcophaga peregrina (Diptera: Sarcophagidae)

doi: 10.3390/insects16080754

Figure Lengend Snippet: Morphological changes during pupal development of Sarcophaga peregrina from day 1 to day 10.

Article Snippet: The input included significantly differentially expressed miRNAs and a custom Sarcophaga peregrina Unigene transcriptome database.

Techniques:

Journal: Insects

Article Title: Temporal miRNA Biomarkers for Pupal Age Estimation in Sarcophaga peregrina (Diptera: Sarcophagidae)

doi: 10.3390/insects16080754

Figure Lengend Snippet: Comprehensive analysis of miRNA expression dynamics during pupal development in Sarcophaga peregrina . ( a ) Boxplot of log 10 (TPM + 1) shows increasing miRNA expression from P1 to P5, with individual dots representing sample-level expression values. ( b ) Density plots indicate a shift toward higher expression levels in P3 and P5. ( c ) PCA reveals clear stage-specific clustering, with PC1 explaining 50.48% of variance. ( d ) Pearson correlation heatmap shows high within-group similarity and intergroup divergence, with circle size and color intensity indicating the strength of correlation between samples.

Article Snippet: The input included significantly differentially expressed miRNAs and a custom Sarcophaga peregrina Unigene transcriptome database.

Techniques: Expressing

Journal: Insects

Article Title: Temporal miRNA Biomarkers for Pupal Age Estimation in Sarcophaga peregrina (Diptera: Sarcophagidae)

doi: 10.3390/insects16080754

Figure Lengend Snippet: Differentially expressed miRNAs across pupal stages in Sarcophaga peregrina . ( a ) Venn diagram showing overlapping differentially expressed miRNAs between P3 vs. P1 and P5 vs. P3 comparisons. ( b ) Bar chart of upregulated and downregulated miRNA counts in each comparison. ( c , e ) Heatmaps of differentially expressed miRNAs in P3 vs. P1 and P5 vs. P3 groups, respectively. ( d , f ) Volcano plots displaying the magnitude and significance of expression changes. Some miRNAs show log 2 FC > 6–8, indicating strong stage-specific regulation. Gray vertical lines indicate the threshold of |log 2 FoldChange| = 1 used to define differential expression.

Article Snippet: The input included significantly differentially expressed miRNAs and a custom Sarcophaga peregrina Unigene transcriptome database.

Techniques: Comparison, Expressing, Quantitative Proteomics

Journal: Insects

Article Title: Temporal miRNA Biomarkers for Pupal Age Estimation in Sarcophaga peregrina (Diptera: Sarcophagidae)

doi: 10.3390/insects16080754

Figure Lengend Snippet: Functional enrichment of predicted target genes of differentially expressed miRNAs in Sarcophaga peregrina pupae. ( a ) Gene Ontology (GO) enrichment of P3 vs. P1 target genes, showing the top 30 significant terms across biological processes (BP), molecular functions (MF), and cellular components (CC). ( b ) KEGG pathway enrichment for P3 vs. P1 targets, highlighting involvement in MAPK, Wnt, Hippo, and ecdysone signaling pathways, as well as glycolysis/gluconeogenesis. ( c ) GO enrichment of P5 vs. P3 target genes, emphasizing roles in redox balance, hypoxia response, and autophagy. ( d ) KEGG pathway enrichment for P5 vs. P3 targets, with strong enrichment in HIF-1, FoxO, autophagy, and oxidative phosphorylation pathways.

Article Snippet: The input included significantly differentially expressed miRNAs and a custom Sarcophaga peregrina Unigene transcriptome database.

Techniques: Functional Assay, Protein-Protein interactions, Phospho-proteomics

Journal: Insects

Article Title: Temporal miRNA Biomarkers for Pupal Age Estimation in Sarcophaga peregrina (Diptera: Sarcophagidae)

doi: 10.3390/insects16080754

Figure Lengend Snippet: Time-series clustering of differentially expressed miRNAs in Sarcophaga peregrina pupae using STEM. ( a ) STEM clustering identified 16 temporal profiles; only Profile 11 showed significant enrichment (FDR = 0.027). ( b ) Line plot of Profile 11 showing a consistent upregulation trend from P1 to P5. ( c ) Heatmap of the 18 miRNAs assigned to Profile 11, most of which exhibit increasing abundance over time. Different colored lines represent individual miRNAs within Profile 11 and are used solely for visual distinction.

Article Snippet: The input included significantly differentially expressed miRNAs and a custom Sarcophaga peregrina Unigene transcriptome database.

Techniques:

Journal: International Journal of Molecular Medicine

Article Title: A type 2 diabetes-associated SNP in KCNQ1 (rs163184) modulates the binding activity of the locus for Sp3 and Lsd1/Kdm1a, potentially affecting CDKN1C expression

doi: 10.3892/ijmm.2017.3273

Figure Lengend Snippet: Effect of SP3 knockdown on the expression of KCNQ1 and nearby genes. Cell lines were transfected with control siRNA or siRNA that targeted human SP3 . Gene expression levels were determined by reverse transcription-quantitative polymerase chain reaction analysis and normalized to β-actin. The expression level of each gene using negative control siRNA was designated as 1.0 in each cell line. The data for TRPM5 and SLC22A18AS from all cell lines, as well as the data for KCNQ1 and OSBPL5 from Caco-2 cells, have been excluded because of the limit of detection. * P<0.01 vs. negative control siRNA samples. siRNA, small interfering RNA; NR, non-risk.

Article Snippet: TaqMan Gene Expression assays for SP3 (UniGene ID, Hs01595811_m1), CD81 molecule ( CD81 ; UniGene ID, Hs01002167_m1), tumor suppressing subtransferable candidate 4 ( TSSC4 ; UniGene ID, Hs00185082_m1), transient receptor potential cation channel subfamily M member 5 ( TRPM5 ; UniGene ID, Hs00175822_m1), KCNQ1 (UniGene ID, Hs00165003_m1), KCNQ1OT1 (UniGene ID, Hs03665990_s1), CDKN1C (UniGene ID, Hs00175938_m1), solute carrier family 22 member 18 ( SLC22A18 ; UniGene ID, Hs00180039_m1), SLC22A18 anti-sense ( SLC22A18AS ; UniGene ID, Hs00757934_m1), pleckstrin homology like domain family A member 2 ( PHLDA2 ; UniGene ID, Hs00169368_m1), nucleosome assembly protein 1-like 4 ( NAP1L4 ; UniGene ID, Hs00924275_m1), cysteinyl-tRNA synthetase ( CARS ; UniGene ID, Hs01000965_m1), oxysterol binding protein like 5 ( OSBPL5 ; UniGene ID, Hs00957760_m1), MAS related GPR family member G ( MRGPRG ; UniGene ID, Hs01010229_s1) and ACTB (UniGene ID, 4352935) were obtained from Applied Biosystems (Thermo Fisher Scientific, Inc.).

Techniques: Knockdown, Expressing, Transfection, Control, Gene Expression, Reverse Transcription, Real-time Polymerase Chain Reaction, Negative Control, Small Interfering RNA