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RNA II

RNA II: A crucial molecular player in gene expression and regulation.
This versatile RNA species is involved in various cellular processes, including transcription, splicing, and post-transcriptional modifications.
Researchers leverage advanced techniques and technologies, such as AI-powered platforms, to optimize and streamline RNA II-related experiments, enhancing reproducibility and driving scientific discovery forward.
By leveraging intelligent comparisons and AI-assisted analysis, researchers can identify the best protocols and products, accelerating their RNA II research and unlocking new insights into this dynamic and complex biomolecule.

Most cited protocols related to «RNA II»

CHIKVs were isolated from either human serum or CSF (
Table 1).
A. albopictus C6/36 cells were inoculated with 1 ml of serum or CSF diluted 1:10 in Leibovitz-L15 medium (Invitrogen/Gibco, Carlsbad, California, United States). The cells were grown at 28 °C in Leibovitz-L15 medium supplemented with 5% heat-inactivated foetal bovine serum (FBS) and 10% tryptose-phosphate. Cells and supernatants were harvested after the first passage (5 d) and the second passage (7 d). The virus isolates were identified as CHIKV by indirect immunofluorescence using anti-CHIKV HMAF. In the case of clinical isolates 05.115, 06.21, 06.27, and 06.49, whose genomes were sequenced, absence of yellow fever virus, dengue type-1 virus, and West Nile virus was confirmed by immunofluorescence assay using specific HMAF.
Extraction of viral RNA from the CHIKV isolates was performed using the NucleoSpin RNA II kit (Machery-Nagel, Düren, Germany) or the QIAAmp Viral Minikit (Qiagen, Courtaboeuf Cedex, France) according to manufacturer's recommended procedures. The sequence of the non-structural region of isolates 05.115, 06.21, 06.27, and 06.49 was determined from RNA extracted from supernatants harvested after the second passage. All other CHIKV isolates sequences were obtained using template RNA extracted from the first passage. Extraction of viral RNA from biological specimens was performed using the QIAAmp Viral Minikit.
Publication 2006
Biopharmaceuticals Cedax Cells Dengue Virus Fetal Bovine Serum Genome Homo sapiens Immunofluorescence Indirect Immunofluorescence L15 culture medium MAFG protein, human Phosphates RNA, Viral RNA II Serum tryptose Virus West Nile virus Yellow fever virus
Total RNA was isolated from mucosa scraping samples using Clontech Total RNA isolation NucleoSpin® RNA II kit (Clontech Laboratories, Inc., CA, USA). One microgram of total RNA, 11mer oligo mix from Fluoresentric, and M-MLV Reverse Transcriptase (Life Technologies, Grand Island, NY, USA) were used to synthesize cDNA according to the manufacturers’ instructions. The relative mRNA levels of mucin 2 (MUC2), fatty acid-binding protein (FABP) 2, FABP6, interleukin (IL)-8, IL-1β, transforming growth factor (TGF)-β4, occludin, zonula occluden (ZO)-1, junctional adhesion molecule (JAM) 2, JAM3, catenin, tumor necrosis factor (TNF) α, Toll-like receptor (TLR) 2β, TLR4, and claudin 1 were measured by quantitative PCR using Applied Biosystems® SYBR® Green PCR Master Mix, the 7500 Fast Real-Time PCR System, and primers in Table 2. Results were expressed as the level relative to the corresponding housekeeping gene actin. All primers were verified for the efficiency and linearity of amplification.
Publication 2015
Actins Catenins Claudin-1 DNA, Complementary FABP2 protein, human Genes, Housekeeping IL1B protein, human Interleukin-8 isolation Junctional Adhesion Molecule B Mucin-2 Mucous Membrane Occludin Oligonucleotide Primers Oligonucleotides RNA, Messenger RNA-Directed DNA Polymerase RNA II SYBR Green I Tight Junctions Toll-Like Receptors transforming growth factor beta4 Tumor Necrosis Factor-alpha
DNA templates (IDT) were synthesized for tRNAPhe, TPP riboswitch, E. coli 5S, hepatitis C virus IRES domain, T. thermophila group I intron, or O. iheyensis group II intron RNAs in the context of flanking 5' and 3' structure cassettes. Templates were amplified by PCR and transcribed into RNA using T7 RNA polymerase43 . RNAs were purified by denaturing polyacrylamide gel electrophoresis, appropriate regions excised, and RNAs passively eluted from the gel overnight at 4 °C. 16S and 23S rRNAs were isolated from DH5α cells during mid-log phase using non-denaturing conditions38 (link). For each sample, 5 pM of RNA was refolded in 100 mM HEPES, pH 8.0, 100 mM NaCl, and 10 mM MgCl2 in a final volume of 10 µL. After folding, RNAs were modified in the presence of 10 mM SHAPE reagent and incubated at 37 °C for 3 min (1M6 and 1M7) or 22 min (NMIA). No-reagent controls, containing neat DMSO rather than SHAPE reagent, were performed in parallel. To account for sequence-specific biases in adduct detection, RNAs were modified using NMIA, 1M7, or 1M6 under strongly denaturing conditions in 50 mM HEPES (pH 8.0), 4 mM EDTA, and 50% formamide at 95 °C. Following modification, RNAs were isolated using either RNA affinity columns (RNeasy MinElute; Qiagen) or G-50 spin columns (GE Healthcare).
Publication 2014
Cells Edetic Acid Escherichia coli formamide Hepatitis C virus HEPES Internal Ribosome Entry Sites Introns Magnesium Chloride methylisoamylnitrosamine Phenylalanine-Specific tRNA Polyacrylamide Gel Electrophoresis Riboswitch RNA, Ribosomal, 23S RNA II Sensitivity Training Groups Sodium Chloride Sulfoxide, Dimethyl
Detailed description of the RNA-isolation has been described previously [16 (link), 17 (link)]; briefly, RNA was isolated from 30 μm sections using RNA-Bee® according to the manufacturer’s instructions (Tel-Test Inc., USA). Quality and quantity of RNA before and after genomic DNA (gDNA) removal and clean-up with the NucleoSpin RNA II tissue kit (Macherey-Nagel GmbH & Co. KG, Germany) were assessed with the Nanodrop ND-1000 (Thermo Scientific, Wilmington, USA) and the MultiNA Microchip Electrophoresis system (Shimadzu, Kyoto, Japan). RNA Integrity Numbers (RIN) were assessed using the MultiNA Microchip Electrophoresis system after gDNA removal and clean-up (Additional file 2 evaluates the relation between Agilent’s BioAnalyzer RIN value and the quality as measured by MultiNA). cDNA was generated from 1 μg total RNA with the RevertAid H Minus First Strand cDNA synthesis kit according to the manufacturer’s instructions (Fermentas, St Leon-Rot, Germany). RT-qPCR was performed with the Mx3000P QPCR machine (Agilent Technologies, the Netherlands) using ABgene Absolute Universal or Absolute SYBR Green with ROX PCR reaction mixtures (Thermo Scientific, USA) according to the manufacturer’s instructions. The intron-spanning assays to quantify levels of 33 transcripts by the delta-delta Cq method were assessed as described before [16 (link), 17 (link)] and are summarized in Additional file 3.
For RNA-seq, 500 ng of total RNA after gDNA removal, clean-up and removing ribosomal RNA using Ribo Zero (Illumina, USA), was used as input for the Illumina TruSeq stranded RNA-seq protocol (paired-end). No biological replicates were used. Libraries were pooled and sequenced on Illumina HiSeq2500 (2x101bp, 177 samples) or NextSeq (2x76bp, 86 samples) instruments. Pool sizes and the amount of samples per run were determined based on the percentage of tumor cells estimated from histological examination [15 (link)]. We used the STAR [18 (link)] algorithm (version 2.4.2a) to align the RNA-seq data on the GRCh38 reference genome (settings are in Additional file 4). To obtain read counts for each gene, the ‘quantMode GeneCounts’ was used, in which only those reads that have a sufficient alignment score and those that are uniquely mapped are included. The 76 bp read length from the NextSeq machine was more than sufficient for accurate mapping to the reference genome, and we found no bias in data originating from the different machines.
Gene annotation was derived from GENCODE Release 23 (https://www.gencodegenes.org/). To obtain exon specific counts for CDK1 and MKI67, all unique HAVANA exons for each gene were extracted and used in FeatureCounts [19 (link)] with the following settings “–t exon”, -O and –f. These settings, and the absence of –p (for paired-end counting), ensures that reads that overlap multiple exons are counted for each of these exons. This ensured all evidence for the presence of an exon was counted.
Publication 2018
Anabolism Biological Assay Biopharmaceuticals CDK1 protein, human Cells DNA, Complementary DNA Chips Electrophoresis Electrophoresis, Microchip Exons Gene Annotation Genes Genome Introns isolation MKI67 protein, human Neoplasms Ribosomal RNA RNA-Seq RNA II SYBR Green I Tissues
Frozen tissues from NSCLC tumors resected at MDACC were used to generate multiple 5-micron thick sections. Representative tissue sections were hematoxylin and eosin (H&E)-stained and reviewed to estimate the percentage of tumor and non-malignant cells. About 5–10 sections were processed to extract RNA, whose quality was assessed on Nano Series II RNA LAB-chips using Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Santa Clara, CA). Cases were selected with the following defined characteristics: tumor (vs. non-malignant) ≥ 70%, malignant cells (vs. stromal cells) ≥ 30%, RNA Integrity Number (RIN) ≥ 4 (range 0–10). RNA samples were shipped to UT Southwestern for expression profiling. Five hundred nanograms of RNA were labeled and hybridized to the Illumina Beadchip array HumanWG-6 V3 (San Diego, CA). Array data were pre-processed using the R package mbcb (15 (link)) for background correction. The arrays were then log-transformed and quantile-normalized. This dataset was submitted to Gene Expression Omnibus (GEO) under the accession GSE41271.
Publication 2016
Cells DNA Chips Eosin Freezing Gene Expression Neoplasms Non-Small Cell Lung Carcinoma RNA II Stromal Cells Tissues

Most recents protocols related to «RNA II»

RNA was extracted from 0.4 to 1 million cells using the Nucleospin RNA II kits (#740955.50; Macherey-Nagel). cDNA was synthesized using random primers (#48190-011; Invitrogen) from 0.1 μg RNA using Superscript III Reverse transcriptase (#18080044; Thermo Fisher Scientific). Real-time qPCR (RT-qPCR) was carried out in 20 μl reactions using SYBR Green I Master (#4887352001; Roche). Primers used were as follows: IFNL1 (Fwd: 5′-GGT​GAC​TTT​GGT​GCT​AGG​CT, Rev: TGA​GTG​ACT​CTT​CCA​AGG​CG-3′), IFNB (Fwd: 5′-GTC​TCC​TCC​AAA​TTG​CTC​TC, Rev: ACA​GGA​GCT​TCT​GAC​ACT​GA-3′), ACTB (Fwd: 5′-GGA​CTT​CGA​GCA​AGA​GAT​GG, Rev: AGC​ACT​GTG​TTG​GCG​TAC​AG-3′), B2M (Fwd: 5′-TCT​CTG​CTG​GAT​GAC​GTG​AG, Rev: TAG​CTG​TGC​TCG​CGC​TAC​T-3′).
Publication 2023
Cells DNA, Complementary Interferon, beta Oligonucleotide Primers RNA-Directed DNA Polymerase RNA II SYBR Green I
Cultured human T cells after treatment were flash frozen in Buffer RLT (Qiagen, 79216) and kept in −80 °C until processing. Total RNA was extracted with the NucleoSpin RNA kit (Macherey-Nagel, 740955). One microgram (1 μg) total RNA was used as an input for mRNA isolation (NEB E7490S), followed by library preparation using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (NEB E7760). Quantification of the libraries was done by Qubit and TapeStation. Paired-end sequencing of the libraries was performed on Nextseq 550. De-multiplexing of samples was done with Illumina’s bcl2fastq software. The fastq files were next aligned to the human genome (hg38) using STAR111 (link) and the transcriptome alignment and gene counts were obtained with HTseq112 (link). Aligned gene counts were normalized to fragments per kilobase of transcript per million mapped reads (log10(FPKM)) using the fpkm function in DESeq2 R package113 (link) (1.32.0). Genes with low counts (<10) were filtered before performing statistical analysis. Differential expression analysis of bulk RNA-Seq data between NANA-treated samples and control was performed using the DESeq2 R package (P-value adjusted to multiple hypothesis testing ≤0.050), while accounting for inter-sample differences. Significantly upregulated genes (adjusted P-value <0.050, log2-fold change >0.250) and downregulated genes (adjusted P-value <0.050, log2-fold change < –0.250) were determined. Up- and downregulated gene lists were separately functionally annotated with gene sets defined by the KEGG and Gene Ontology databases (org.Hs.eg.db, version 3.5.0), using enrichGO and enrichKEGG functions in R package clusterProfiler (3.6.0), using the hypergeometric P-value and FDR correction for multiple hypothesis (with a threshold of FDR < 0.050).
Publication 2023
Aftercare Buffers Dietary Fiber DNA Library Freezing Genes Genome, Human Homo sapiens isolation RNA, Messenger RNA-Seq RNA II T-Lymphocyte Transcriptome
The library preparation and RNA-sequencing were performed by Novogene Corporation Inc., (Sacramento, CA). The RNA-seq libraries were constructed using NEBNext UltraTM II RNA Library Prep Kit for Illumina and were sequenced by Novaseq 6,000 PE150 system. Raw reads of FASTQ format were firstly processed through fastp, and clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. All the downstream analyses were based on the clean data with high quality. The raw RNA-seq raw data were trimmed to remove the adapter sequences (GAT​CGG​AAG​AGC​ACA​CGT​CTG​AAC​TCC​AGT​CAC​GGT​CTA​CTA​TCT​CGT​ATG​CCG​TCT​TCT​GCT​TG and AGA​TCG​GAA​GAG​CGT​CGT​GTA​GGG​AAA​GAG​TGT​AGA​TCT​CGG -TGGTCGCCGTATCATT) with command-line tool cutadapt (1.8.1). Then the trimmed files were aligned with Tophat (version 2.0.9) to GRCh37/hg19 Homo sapiens reference genome. The human gene symbols and their raw counts were calculated using the HTSeq (version 0.6.1p1) package in Python with the hg19 Homo sapiens gtf file. Differential gene-expression analysis was performed using the edgeR package in R, and the normalization was performed using a trimmed mean of M-values (TMM) method across all samples. The Gene Ontology (GO) enrichment analysis was performed using on-line tools DAVID (version 6.8) (https://david.ncifcrf.gov/summary.jsp) and the Gene Ontology Resource (http://geneontology.org). The Gene Ontology (GO) enrichment analysis of differentially expressed genes was performed using DAVID (https://david.ncifcrf.gov).
Publication 2023
DNA Library Gene Expression Profiling Genes Genome Homo sapiens Poly A Python RNA-Seq RNA II
Total RNA was extracted from the patient FNA samples, the resulting BL cell lines, and NSG-BL mouse tumors using the Monarch Total RNA extraction kit (New England Biolabs). Starting with 1–5 µg total RNA, we enriched mRNA molecules using oligo-dT magnetic beads to capture polyA-tailed mRNA molecules. We then proceeded to prepare strand-specific RNA-seq libraries following the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB). Final library concentration and fragment size were confirmed with a Qubit 4 fluorometer (Thermo Fisher Scientific) and fragment analyzer (Agilent), respectively. These libraries were sequenced with paired-end reads (2 × 75 bp) on the NextSeq 550 system (Illumina, Inc.). Raw sequencing data files from this study are deposited in the NCBI’s database of Genotypes and Phenotypes (dbGaP) with accession number phs001282.v2.p1.
Publication 2023
Cell Lines DNA Library Genotype mRNA, Polyadenylated Mus Neoplasms oligo (dT) Patients Phenotype RNA, Messenger RNA-Seq RNA II

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Publication 2023
DNA, Viral Endopeptidase K Nucleic Acids Real-Time Polymerase Chain Reaction Reverse Transcriptase Polymerase Chain Reaction RNA II SARS-CoV-2 Virus

Top products related to «RNA II»

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The NucleoSpin RNA II kit is a laboratory tool designed for the isolation and purification of total RNA from a variety of biological samples. It utilizes a silica-membrane technology to efficiently capture and purify RNA molecules.
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NucleoSpin RNA II is a product from Macherey-Nagel designed for the isolation of total RNA from various biological samples. It utilizes a silica-membrane-based technology to efficiently capture and purify RNA molecules.
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The NEBNext Ultra II Directional RNA Library Prep Kit is a laboratory equipment product designed for the preparation of RNA samples for next-generation sequencing. The kit provides a streamlined workflow for the conversion of RNA into directional sequencing libraries.
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The Agilent 2100 Bioanalyzer is a lab instrument that provides automated analysis of DNA, RNA, and protein samples. It uses microfluidic technology to separate and detect these biomolecules with high sensitivity and resolution.
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The NEBNext Poly(A) mRNA Magnetic Isolation Module is a laboratory equipment product designed to isolate and purify mRNA from total RNA samples. The module utilizes magnetic beads coated with oligo(dT) to selectively capture and separate polyadenylated mRNA molecules from the total RNA pool.
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The RNeasy Mini Kit is a laboratory equipment designed for the purification of total RNA from a variety of sample types, including animal cells, tissues, and other biological materials. The kit utilizes a silica-based membrane technology to selectively bind and isolate RNA molecules, allowing for efficient extraction and recovery of high-quality RNA.
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The NovaSeq 6000 is a high-throughput sequencing system designed for large-scale genomic projects. It utilizes Illumina's sequencing by synthesis (SBS) technology to generate high-quality sequencing data. The NovaSeq 6000 can process multiple samples simultaneously and is capable of producing up to 6 Tb of data per run, making it suitable for a wide range of applications, including whole-genome sequencing, exome sequencing, and RNA sequencing.
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TRIzol reagent is a monophasic solution of phenol, guanidine isothiocyanate, and other proprietary components designed for the isolation of total RNA, DNA, and proteins from a variety of biological samples. The reagent maintains the integrity of the RNA while disrupting cells and dissolving cell components.
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The 2100 Bioanalyzer is a lab equipment product from Agilent Technologies. It is a microfluidic platform designed for the analysis of DNA, RNA, and proteins. The 2100 Bioanalyzer utilizes a lab-on-a-chip technology to perform automated electrophoretic separations and detection.

More about "RNA II"

Explore the Versatile World of RNA II: A Crucial Player in Gene Expression and Regulation RNA II, also known as nuclear RNA or heterogeneous nuclear RNA (hnRNA), is a crucial molecular player in the intricate process of gene expression and regulation.
This versatile RNA species is involved in a wide range of cellular processes, including transcription, splicing, and post-transcriptional modifications.
Researchers leveraging advanced techniques and technologies, such as AI-powered platforms like PubCompare.ai, are streamlining and optimizing their RNA II-related experiments.
By utilizing intelligent comparisons and AI-assisted analysis, scientists can identify the best protocols and products, enhancing reproducibility and driving scientific discovery forward.
When it comes to RNA II research, the NucleoSpin RNA II kit and NucleoSpin RNA II products from Macherey-Nagel offer a reliable and efficient solution for RNA extraction and purification.
The NEBNext Ultra II Directional RNA Library Prep Kit from New England Biolabs (NEB) enables the construction of high-quality RNA-seq libraries, while the Agilent 2100 Bioanalyzer provides valuable insights into the quality and integrity of RNA samples.
The NEBNext Poly(A) mRNA Magnetic Isolation Module from NEB allows for the selective isolation of polyadenylated mRNA from total RNA, while the RNeasy Mini Kit from Qiagen is a popular choice for purifying high-quality RNA from a variety of sample types.
To power your RNA II research, the NovaSeq 6000 from Illumina and the NextSeq 500 from Illumina offer high-throughput sequencing capabilities.
Additionally, the TRIzol reagent from Thermo Fisher Scientific is a widely used solution for the extraction and isolation of RNA, DNA, and proteins from a variety of sample sources.
By leveraging these cutting-edge technologies and techniques, researchers can unlock new insights into the dynamic and complex world of RNA II, driving scientific progress and expanding our understanding of gene expression and regulation.