poly a enrichment  (Novogene)

Journal: bioRxiv

Article Title: Human vault RNAs exhibit diverse expression patterns and inter-locus compensation

doi: 10.64898/2026.06.17.732918

Figure Lengend Snippet: Quantification of vtRNA1-1 (red), 1-2 (blue), 1-3 (green), and 2-1 (purple) relative expression across HEK293T cell lines via RT-qPCR. Values correspond to ΔΔC q , which is calculated as vtRNA C q normalized to GAPDH, then knockout ΔC q normalized to wild-type (“HEK293T”) for each paralog. Data points are RNA samples from independent biological replicates, and error bars indicate mean ± standard deviation. Dashed grey line is a visual aid for no expression change, and dotted grey lines are a composite statistical threshold (p<0.05 in a two-sample t-test, assuming n=3 per group and variances equivalent to the “HEK293T” samples). Corresponding Northern blots are in Supplemental Figure 4. * Gene has a small, off-target deletion in its flanking sequence, identified in Supplemental Figure 2.

Article Snippet: To probe for more subtle vtRNA-knockout effects, we isolated total RNA samples from our wild-type (HEK293T), CTRLdel, vt1-1 KO, vt1-2 KO, vt1-3 KO, and vt1-TKO cell lines and submitted them for (poly-A enrichment) RNA sequencing (Plasmidsaurus).

Techniques: Expressing, Quantitative RT-PCR, Knock-Out, Standard Deviation, Northern Blot, Sequencing

Journal: bioRxiv

Article Title: Human vault RNAs exhibit diverse expression patterns and inter-locus compensation

doi: 10.64898/2026.06.17.732918

Figure Lengend Snippet: [a] Principal components analysis (PCA) of RNA-seq transcript counts per million transcripts (CPM) data for each HEK293T cell line. Data points correspond to RNA samples from independent biological replicates. [b] Volcano plots of transcripts differentially expressed between genetically edited cell lines and wild-type (WT) HEK293T. Upregulated (blue) and downregulated (red) transcripts have FDR < 0.05 (false discovery rate), and log 2 |FC| ≥ 1 (fold change), and their numbers are reported (“n”) for each differential expression analysis. The GAPDH and UBC transcripts (“Housekeeping”, purple) are shown as controls. Transcripts encoding proteins associated with vtRNA binding (“vtRNA Binders”, green) correspond to proteins previously identified by vtRNA pulldown .

Article Snippet: To probe for more subtle vtRNA-knockout effects, we isolated total RNA samples from our wild-type (HEK293T), CTRLdel, vt1-1 KO, vt1-2 KO, vt1-3 KO, and vt1-TKO cell lines and submitted them for (poly-A enrichment) RNA sequencing (Plasmidsaurus).

Techniques: RNA Sequencing, Quantitative Proteomics, Binding Assay

Journal: bioRxiv

Article Title: Biomimetic miR-133a inhibitor activated scaffolds optimised for spinal cord repair promote neurite outgrowth and angiogenesis via neuronal cytoskeletal remodelling

doi: 10.64898/2026.04.22.719922

Figure Lengend Snippet: A) Venn diagram of predicted miR-133a targets identified across three public miRNA–mRNA interaction databases (TargetScan, miRDB and StarBase), showing the shared gene set used for downstream enrichment analysis. B) Gene Ontology (GO) enrichment analysis of common predicted miR-133a targets, highlighting over-represented neuronal and cytoskeletal categories. C) KEGG pathway enrichment analysis of the same gene set, demonstrating enrichment of pathways linked to synaptic vesicle cycling, regulation of the actin cytoskeleton and adherens junctions. D-E) Size distribution spectra of fresh and lyophilised RALA/miR-133a-i nanoparticles formulated at an N:P 8 ratio. Insert summarises z-average, polydispersity index (PDI), mean count rate and zeta potential +/- SEM. F) Mean hydrodynamic size and PDI of fresh and lyophilised RALA/miR-133a-i nanoparticles at N:P ratio of 8. G) Ion exchange chromatography results showing absorbance spectra of RALA/ miR-133a-i nanoparticles, water and unencapsulated miRNA following chromatography through an anionic Sephadex resin. H) Encapsulation efficiency of RALA/miR-133a-i nanoparticles measured by quantifying free miRNA present in solution. I) TEM image showing RALA/miR-133a-i nanoparticles. J) Loading efficiency of >96% of nanoparticles in hyaluronic acid scaffolds was detected by the Ribogreen Assay. Nanoparticle release kinetics measured in ng and percentage change for short-term release (K-L) and long-term release periods (M-N) demonstrated an initial burst release followed by a slower, consistent release.

Article Snippet: Libraries were prepared and sequenced by Novogene (UK) using poly(A)-enriched mRNA libraries and a NovaSeq X Plus platform (paired-end 150 bp; N=4 untreated, N=5 miR-133a-i-activated).

Techniques: Zeta Potential Analyzer, Ion Exchange Chromatography, Chromatography, Encapsulation