Journal: The Plant journal : for cell and molecular biology

Article Title: The PPR-SMR protein PPR53 enhances the stability and translation of specific chloroplast RNAs in maize.

doi: 10.1111/tpj.13093

Figure Lengend Snippet: Figure 5. Analysis of chloroplast rRNAs in ppr53 mutants. (a) RNA gel blot analysis of transcripts from the rrn transcription unit. Replicate blots of seedling leaf RNA were hybridized to the probes indicated on the map. Three heteroallelic ppr53 individuals with distinct pigment phenotypes (iv vir, vpyg vir and vir; see Figure 1) were analyzed. RNAs from the non-photosynthetic mutants atp4 and wtf2 were analyzed for comparison. The wtf2 mutant is shown to illustrate pleiotropic effects resulting from the loss of plastid ribosomes. An image of one of the blots stained with methylene blue is shown below to illustrate equal loading of cytosolic 28S and 18S rRNAs. (b) Primer extension assay to quantify processed transcripts with a 50-end mapping 70 nucleotides upstream of rrn23. A 50-end labeled 24-nucleotide primer starting four nucleotides upstream of mature 23S rRNA was used to prime reverse transcription on 5 lg of seedling leaf RNA. The ribosome-deficient mutant wtf2 (see panel a) as well as two other non-photosynthetic mutants (atp4 and crp1) accumulate increased levels of the 70 23S rRNA precursor (see arrow), whereas it is undetectable in all three ppr53 mutant individuals. The abundance of longer rrn23 processing intermediates is similar in all mutant samples ana- lyzed, as shown also on the RNA gel blot in panel (a) (see probe 2 data). (c) PPR53-dependent sRNA mapping to the 50-end of the PPR53-dependent rrn23 precursor. Screen captures from the Integrated Genome Viewer show reads as pink lines and a histogram of read counts in gray (above). The 50-end of the PPR53-dependent sRNAs corresponds to that of the PPR53-dependent pre-23S rRNA. The sRNA reads from flanking regions serve as internal standards. Data from a ppr4 mutant are shown to control for effects resulting from the loss of plastid ribosomes. The loss of this PPR53-dependent sRNA is accompanied by an increase in the abundance of an sRNA with a 50-end two nucleotides upstream. The basis for this effect is unknown.

Article Snippet: Sequencing libraries were prepared with the NEBNext Multiplex Small RNA Library Prep Set.

Techniques: Western Blot, Comparison, Mutagenesis, Staining, Primer Extension Assay, Labeling, Reverse Transcription, Control

Journal: Frontiers in Genetics

Article Title: LuluDB—The Database Created Based on Small RNA, Transcriptome, and Degradome Sequencing Shows the Wide Landscape of Non-coding and Coding RNA in Yellow Lupine ( Lupinus luteus L.) Flowers and Pods

doi: 10.3389/fgene.2020.00455

Figure Lengend Snippet: Relationship between next-generation sequencing and qPCR results. (A) Log 2 fold change of gene expression assessed using NGS plotted against log 2 fold change of gene expression assessed using qPCR. (B) The same plot for sRNA data. R 2 is coefficient of determination, ρ is Spearman's rank correlation coefficient. (C) Graphs showing the similar trend in expression levels of miRNAs and siRNAs assessed with NGS and qPCR.

Article Snippet: After passing all quality and quantity checks (as described in Glazinska et al., ), total RNA was used for preparation of small RNA libraries using NEBNext Multiplex Small RNA Library Prep kit for Illumina (New England Biolabs, Ipswich, MA, USA) and subsequently sequenced on the HiSeq4000 platform (Illumina, San Diego, CA, USA) in the 50 single-end mode.

Techniques: Next-Generation Sequencing, Gene Expression, Expressing

Journal: The Science of the Total Environment

Article Title: Sampling methods and assays applied in SARS-CoV-2 exposure assessment

doi: 10.1016/j.scitotenv.2021.145903

Figure Lengend Snippet: Data obtained from the chosen articles.

Article Snippet: , 43. Aerosol and surface contamination of SARS-CoV-2 observed in quarantine and isolation care , USA , No , Surface and air samples from COVID-19 patient rooms , Air sampling: Sartorius Airport MD8 air sampler operating at 50 Lpm for 15 min. Surface samples: sterile swabs , Viral RNA Extractions: using a Qiagen DSP Virus Spin Kit. RT-qPCR: using Invitrogen Superscript III Platinum One-Step Quantitative RT-qPCR System. Primers and probe used target the E gene of SARS-CoV-2. , • We detected viral contamination among all samples. , ( ) .

Techniques: Sampling, Lysis, RNA Extraction, Environmental Monitoring, Virus, Multiplex Assay, Northern Blot, Marker, RNA Detection, Isolation, Membrane, Control, Environmental Sampling, Amplification, Transmission Assay, Aerosol, Diagnostic Assay, Infection, Sterility, Real-time Polymerase Chain Reaction, Nested PCR, Reverse Transcription, Extraction, Purification, Digital PCR, Preserving, Quantitative RT-PCR, cDNA Synthesis, Magnetic Beads, Incubation, Modification, One Step RT-PCR, Cell Culture, Sequencing

Journal: Cell reports

Article Title: Circulating monocytes associated with anti-PD-1 resistance in human biliary cancer induce T cell paralysis

doi: 10.1016/j.celrep.2022.111384

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: The RNeasy Mini Kit (Qiagen) was used to extract RNA from minimum 2.5 × 10 5 cells per PBMC sample. cDNA was prepared using methods previously described, with the Smart-seq2 protocol , and libraries were prepared using Nextera XT DNA Sample Preparation Kit.

Techniques: Control, Recombinant, Staining, Blocking Assay, Sample Prep, RNAscope, Multiplex Assay, Biomarker Discovery, Software, Cytometry, Microscopy

Journal: Neuron

Article Title: Inhibition of Upf2-Dependent Nonsense-Mediated Decay Leads to Behavioral and Neurophysiological Abnormalities by Activating the Immune Response

doi: 10.1016/j.neuron.2019.08.027

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: RNAeasy Plus Universal Mini Kit , QIAGEN , Cat. #: 73404.

Techniques: Recombinant, Sequencing, SYBR Green Assay, Multiplex Assay, Microarray, Knock-Out, Software