Journal: bioRxiv

Article Title: Genetic inactivation of the Translin/Trax RNase activity alters small RNAs including miRNAs, disrupts gene expression and impairs distinct forms of hippocampal synaptic plasticity and memory

doi: 10.1101/2025.07.10.663777

Figure Lengend Snippet: Volcano plots showing the mature miRNAs differentially expressed in the TraxE126A mutants compared to wildtype littermates as identified by (A) miRNA sequencing and (B) miRNA microarray. Volcano plots showing the differentially expressed small RNA species identified using microarray analysis including (C) Precursor miRNAs (pre-miRNAs), (D) Small nucleolar RNAs (snoRNAs), (E) mature tRNAs and (F) tRNA-derived small RNAs (tsRNAs). In all the plots, the upregulated and downregulated miRNAs (false discovery rate, FDR <0.050 and log 2 fold change ≥0.200) are highlighted in red and blue, respectively. (TraxE126A, n=4; WT, n=5, all males). Largest changes were seen in tsRNA levels (majority are 5’-fragments) and mature miRNAs.

Article Snippet: The labeled RNA species are then hybridized onto Arraystar Small RNA Expression Microarray (8×15K format), scanned by an Agilent G2505C scanner followed by data processing and analysis.

Techniques: Sequencing, Microarray, Derivative Assay

Journal: bioRxiv

Article Title: Genetic inactivation of the Translin/Trax RNase activity alters small RNAs including miRNAs, disrupts gene expression and impairs distinct forms of hippocampal synaptic plasticity and memory

doi: 10.1101/2025.07.10.663777

Figure Lengend Snippet: (A) Venn diagram showing the overlap between mature miRNAs identified using miRNA sequencing and microarray analysis (with FDR<0.050 and log 2 fold change ≥0.200). A total of 12 miRNAs (10 upregulated and 2 downregulated) were found to be common and were used for target prediction using miRDB database. (B) An upset plot showing the shared and unique predicted mRNA target profiles in the miRDB database for the 12 common miRNAs. Only targets with miRDB Target Score ≥60 are included. (C) Top 15 KEGG pathways and (D) Gene Ontology (GO) Biological Process terms from the functional enrichment analysis of the predicted targets of the 12 common miRNAs performed using DAVID database.

Article Snippet: The labeled RNA species are then hybridized onto Arraystar Small RNA Expression Microarray (8×15K format), scanned by an Agilent G2505C scanner followed by data processing and analysis.

Techniques: Sequencing, Microarray, Functional Assay

Journal: Upsala Journal of Medical Sciences

Article Title: From early methods for DNA diagnostics to genomes and epigenomes at high resolution during four decades – a personal perspective

doi: 10.48101/ujms.v129.11134

Figure Lengend Snippet: In-house manufactured modified robot for printing microarrays and silicon rubber reaction chamber for minisequencing reactions: (a) To automate printing of the minisequencing primers on a microscope, a low-cost industrial robot for etching a gluing (Isel Automation, Eiterfeld) was modified with an in-house manufactured tweezer-like tip for printing oligonucleotide primers in circular arrays on microscope slides in a format compatible with multichannel pipets. The robot had a capacity to print minisequencing detection primers for 300 samples per microscope slide. (b) Reusable miniaturized silicon rubber reaction chambers were prepared in-house molded on an inverted 384-well microtiter plate with V-shaped wells as a mold. Liquid silicon rubber (Elastosil RT 601 A/B, Wacker-Chemie GmbH) was poured into the mold, leaving about 1–2 mm of the tip of the wells uncovered. After allowing the rubber to harden over night, the grids containing 384 cone-shaped reaction chambers were cut to match the size of microscope slides. A rubber grid was placed over the primer arrays to form 80 separate reaction chambers. The reaction chambers had a glass surface with the primer array as bottom and the molded cone-shaped silicon rubber as wells, with open tops for pipet tips to fit into the chambers. Prior to adding the reaction mixtures, the rubber grid is firmly pressed against the glass surface in a custom-made aluminum rack with a Plexiglas cover containing drill holes for the pipet tips, through which the reaction mixtures are added. An aluminum rack, which can be heated, holds three microarrays with 80 reaction chambers.

Article Snippet: We used a microarray format on microscope slides for SNP genotyping with fluorescence detection using four dideoxy nucleotides (ddNTPs) labeled with Tamra (tetramethyl-6-carboxyrhodamine) in four separate reaction mixtures (NEN Life Science Products).

Techniques: Modification, Microscopy

Journal: Upsala Journal of Medical Sciences

Article Title: From early methods for DNA diagnostics to genomes and epigenomes at high resolution during four decades – a personal perspective

doi: 10.48101/ujms.v129.11134

Figure Lengend Snippet: Principle of allele-specific primer extension and genotyping results by allele-specific primer extension: (a) A pair of allele-specific primers with different 3’-ends that are complementary to each mutant or variable SNP allele is immobilized on a microscope slide as small circular arrays (125–150 uM in diameter). The DNA templates are amplified by multiplex PCR. During PC, T7 RNA polymerase promoter is inserted into the 5’-end of the DNA fragments. For genotyping, the PCR products are added to the primer arrays together with ribonucleotides (rNTPs) and a T7 RNA polymerase to generate multiple RNA targets by reverse transcription of each PCR product. Simultaneously with reverse transcription, fluorescent CY5-labeled dNTPs are incorporated into the target molecules in allele-specific primer extension reactions. The fluorescent signals on the microscope slides are quantified using a confocal fluorescence scanner, and the data are interpreted with a custom-designed software. (b) Carrier frequencies of 31 mutations of the ‘Finnish disease heritage’ determined in 2,100 population samples from four geographical regions of Finland.

Article Snippet: We used a microarray format on microscope slides for SNP genotyping with fluorescence detection using four dideoxy nucleotides (ddNTPs) labeled with Tamra (tetramethyl-6-carboxyrhodamine) in four separate reaction mixtures (NEN Life Science Products).

Techniques: Mutagenesis, Microscopy, Amplification, Multiplex Assay, Reverse Transcription, Labeling, Fluorescence, Software

Journal: Upsala Journal of Medical Sciences

Article Title: From early methods for DNA diagnostics to genomes and epigenomes at high resolution during four decades – a personal perspective

doi: 10.48101/ujms.v129.11134

Figure Lengend Snippet: Principle of four color tag-array minisequencing of single nucleotide polymorphisms: (a) Each minisequencing primer contains a unique 5’-tag sequence for capture of the extended primers by an immobilized 3’-complementary (c-tag) oligonucleotide in an ‘array-of-array’ configuration on a microscope slide. C-tag oligonucleotides have been immobilized on CodeLink Activated microarray slides (Motorola) by mediation of a 3’-NH2 group using a ProSys 5,510 spotter (Cartesian). The SNPs to be genotyped are amplified by multiplex PCR, after which cyclic minisequencing reactions in solution are performed with four fluorescently labeled ddNTPs in which the extended detection primers anneal immediately adjacent to each polymorphic SNP position. After genotyping, the fluorescent signals are measured using a ScanArray 5,000 instrument (Perkin Elmer Life Sciences), and the genotypes are assigned using the QuantArray ® analysis software of the instrument. (b) Images obtained by scanning a microscope slide at four wavelengths from one individual genotyped by WGA for a panel of 45 SNPs using tag-array minisequencing. Result from primers in both DNA polarities at duplicate positions is shown. The images from genomic DNA (WGA) and primer extension preamplification (PEP) and MDA products are shown in three vertical rows. The fluorescent labels used for the four dideoxy-dNTPs are indicated above the horizontal rows of the subarrays. The obtained signals are reproduced with an artificial rainbow scale with blue as low and white as saturated signal.

Article Snippet: We used a microarray format on microscope slides for SNP genotyping with fluorescence detection using four dideoxy nucleotides (ddNTPs) labeled with Tamra (tetramethyl-6-carboxyrhodamine) in four separate reaction mixtures (NEN Life Science Products).

Techniques: Sequencing, Microscopy, Microarray, Amplification, Multiplex Assay, Labeling, Software

Journal: Journal of Experimental Botany

Article Title: NAC61 regulates late- and post-ripening osmotic, oxidative, and biotic stress responses in grapevine

doi: 10.1093/jxb/erad507

Figure Lengend Snippet: NAC61 expression analysis. (A) NAC61 expression behavior in grapevine organs throughout development (bar plot) and compared in the heatmap (logarithmic value) with that of NAC60 and NAC33. The data were retrieved from the atlas transcriptomic dataset of cv. ‘Corvina’ ( Fasoli et al ., 2012 ). Each value represents the mean ±SD of three biological replicates. (B) Correlation between NAC61 expression level and sugar content in grape berries sampled from fruit set to maturity in cv. ‘Cabernet Sauvignon’ and cv. ‘Pinot noir’ ( Fasoli et al ., 2018 ). The black line represents the trend of the averaged values of the two varieties. The R 2 values shown correspond to the fitting of different polynomial regressions to each corresponding group of samples (orange for cv. ‘Cabernet Sauvignon’ samples, blue for cv. ‘Pinot noir’ samples, and black for the entire set of samples). (C) Correlation between NAC61 expression level and sugar content in grape berries sampled during post-harvest dehydration in six different varieties ( Zenoni et al ., 2016 ). (D) Correlation between NAC61 expression level and berry weight loss in cv. ‘Corvina’ berries sampled during traditional long and forced short post-harvest dehydration processes ( Zenoni et al ., 2020 ). Expression values were determined by microarray analysis and each value represents the mean ±SD from three biological replicates. (E) NAC61 GCNs based on berry, leaf, and tissue-independent (TI) datasets. Left, Venn diagram showing exclusive and shared genes based on the three datasets; right, three-dimensional plot of co-expressed genes in which NAC, WRKY, and ZIP family members already described as having involvement in berry ripening and/or stress responses are indicated.

Article Snippet: Each sample was hybridized to an Agilent custom microarray four-pack 44K format (Agilent Sure Print HD 4X44K 60-mer; cat. no. G2514F-048771) ( Dal Santo et al. , 2016 ) and scanned using an Agilent Scanner (G2565CA; Agilent Technologies, Santa Clara, CA, USA).

Techniques: Expressing, Microarray

Journal: Non-Coding RNA

Article Title: Possible Involvement of Long Non-Coding RNAs GNAS-AS1 and MIR205HG in the Modulation of 5-Fluorouracil Chemosensitivity in Colon Cancer Cells through Increased Extracellular Release of Exosomes

doi: 10.3390/ncrna10020025

Figure Lengend Snippet: Top ten upregulated lncRNAs and mRNAs and their respective fold-changes and p -values based on the cDNA microarray dataset. The transcripts were statistically analyzed in the Agilent GeneSpring GX (v14.9.1) software using moderated t -test and Benjamin–Hochberg multiple testing corrections and had satisfied the p -value of <0.05 and fold-change cutoff of ±2.00. Data shown are from four independent experiments.

Article Snippet: In this study, purified total RNAs of both the SW480/DR and SW480/DS cells were analyzed using Agilent SurePrint G3 Human Gene Expression v3 8x60k format cDNA microarray and processed in the Agilent GeneSpring GX v14.9.1 software.

Techniques: Microarray, Software

Journal: Non-Coding RNA

Article Title: Possible Involvement of Long Non-Coding RNAs GNAS-AS1 and MIR205HG in the Modulation of 5-Fluorouracil Chemosensitivity in Colon Cancer Cells through Increased Extracellular Release of Exosomes

doi: 10.3390/ncrna10020025

Figure Lengend Snippet: Top ten downregulated lncRNAs and mRNAs and their respective fold-changes and p -values based on the cDNA microarray dataset. The transcripts were statistically analyzed in the Agilent GeneSpring GX (v14.9.1) software using moderated t -test and Benjamin–Hochberg multiple testing corrections and had satisfied the p -value of <0.05 and fold-change cutoff of ±2.00. Data shown are from four independent experiments.

Article Snippet: In this study, purified total RNAs of both the SW480/DR and SW480/DS cells were analyzed using Agilent SurePrint G3 Human Gene Expression v3 8x60k format cDNA microarray and processed in the Agilent GeneSpring GX v14.9.1 software.

Techniques: Microarray, Software

Journal: Non-Coding RNA

Article Title: Possible Involvement of Long Non-Coding RNAs GNAS-AS1 and MIR205HG in the Modulation of 5-Fluorouracil Chemosensitivity in Colon Cancer Cells through Increased Extracellular Release of Exosomes

doi: 10.3390/ncrna10020025

Figure Lengend Snippet: Difference in lncRNA and mRNA fold-changes between the cDNA microarray and in-house RT-qPCR experiments. Data shown are from three independent experiments (in triplicates) with calculated SD values to represent error bars and their statistical analyses were conducted using one-way ANOVA.

Article Snippet: In this study, purified total RNAs of both the SW480/DR and SW480/DS cells were analyzed using Agilent SurePrint G3 Human Gene Expression v3 8x60k format cDNA microarray and processed in the Agilent GeneSpring GX v14.9.1 software.

Techniques: Microarray, Quantitative RT-PCR

Journal: Non-Coding RNA

Article Title: Possible Involvement of Long Non-Coding RNAs GNAS-AS1 and MIR205HG in the Modulation of 5-Fluorouracil Chemosensitivity in Colon Cancer Cells through Increased Extracellular Release of Exosomes

doi: 10.3390/ncrna10020025

Figure Lengend Snippet: ( A ) LncRNA-mRNA interaction network was constructed based on the ten selected candidate lncRNAs from the cDNA microarray dataset. The resulting mRNA interactions were predicted using the “rtool” database with −20 kcal as the minimum energy threshold and were filtered to show only mRNAs that were also dysregulated in the dataset. Data were visualized using Cytoscape v3.8.2. (Pink diamond = candidate lncRNA, blue circle = predicted putative mRNA targets). ( B ) A total of nine mRNAs were identified as both responsible in the “regulated exocytosis” hit as well as highly likely to be regulated by the candidate lncRNAs listed in ( A ). Data were visualized using Cytoscape v3.8.2. (pink diamond = candidate regulator lncRNA, blue circle = mRNA predicted involved in the biological process).

Article Snippet: In this study, purified total RNAs of both the SW480/DR and SW480/DS cells were analyzed using Agilent SurePrint G3 Human Gene Expression v3 8x60k format cDNA microarray and processed in the Agilent GeneSpring GX v14.9.1 software.

Techniques: Construct, Microarray