The RIN: an RNA integrity number for assigning integrity values to RNA measurements

Schröeder, Andreas; Mueller, Odilo; Stöcker, Susanne; Salowsky, Ruediger; Leiber, Michael J.; Gassmann, Marcus; Lightfoot, Samar; Menzel, W. Paul; Granzow, Martin; Ragg, Thomas

doi:10.1186/1471-2199-7-3

Cited by 2,045 publications

(1,063 citation statements)

References 10 publications

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“…RNA integrity (Schroeder et al, 2006) was verified using the Agilent 2100 Bioanalyzer (Agilent Technologies) and all six samples had an RNA integrated number (RIN) value more than 8.0. The samples for transcriptome analysis were prepared using the Illumina kit according to the manufacturer's instructions.…”

Section: Sample Collection and Rna Extractionmentioning

confidence: 99%

De-novo characterization of the soft-shelled turtle Pelodiscus sinensis transcriptome using Illumina RNA-Seq technology

Wang

et al. 2013

J. Zhejiang Univ. Sci. B

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Abstract:The soft-shelled turtle Pelodiscus sinensis is a high-profile turtle species because of its nutritional and medicinal value in Asian countries. However, little is known about the genes that are involved in formation of their nutritional quality traits, especially the molecular mechanisms responsible for unsaturated fatty acid and collagen biosynthesis. In the present study, the transcriptomes from six tissues from Pelodiscus sinensis were sequenced using an Illumina paired-end sequencing platform. We obtained more than 47 million sequencing reads and 73 954 unigenes with an average size of 754 bp by de-novo assembly. In total, 55.19% of the unigenes (40 814) had significant similarity with proteins in the National Center of Biotechnology Information (NCBI) non-redundant protein database and Swiss-Prot database (E-value <10 −5 ). Of these annotated unigenes, 9 156 and 11 947 unigenes were assigned to 52 gene ontology categories (GO) and 25 clusters of orthologous groups (COG), respectively. In total, 26 496 (35.83%) unigenes were assigned to 242 pathways using the Kyoto Encyclopedia of Genes and Genomes pathway database (KEGG). In addition, we found a number of highly expressed genes involved in the regulation of P. sinensis unsaturated fatty acid biosynthesis and collagen formation, including desaturases, growth factors, transcription factors, and extracellular matrix components. Our data represent the most comprehensive sequence resource available for the Chinese soft-shelled turtle and could provide a basis for new research on this turtle as well as the molecular genetics and functional genomics of other terrapins. To our knowledge, we report for the first time, the large-scale RNA sequencing (RNA-Seq) of terrapin animals and would enrich the knowledge of turtles for future research.

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Section: Sample Collection and Rna Extractionmentioning

confidence: 99%

De-novo characterization of the soft-shelled turtle Pelodiscus sinensis transcriptome using Illumina RNA-Seq technology

Wang

et al. 2013

J. Zhejiang Univ. Sci. B

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“…The yield and purity of the extracted RNA were checked using standard protocols of absorbance ratio between 260 and 280 nm, and 1% agarose gel electrophoresis (Farrell 1998a). Furthermore, RIN score of individual samples was determined using Agilent 2100 Bioanalyzer, RNA 6000 Nano LabChip kit, and Agilent 2100 Expert Software (Agilent Technologies, Inc., Santa Clara, CA, USA) (Schroeder et al 2006), and all samples had RIN score O8.0.…”

Section: Rna Extractionmentioning

confidence: 99%

IGF2, IGF binding protein 1, and matrix metalloproteinases 2 and 9 in implantation-stage endometrium following immunoneutralization of vascular endothelial growth factor in the rhesus monkey

Ghosh¹,

Najwa²,

Khan³

et al. 2011

Reproduction

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Blastocyst implantation in the rhesus monkey is inhibited by administration of antibody against vascular endothelial growth factor (VEGF) A during peri-implantation period with no change in the circulatory concentrations of estradiol, progesterone, and VEGF. In this study, we have investigated the effect of administration of a MAB to VEGFA on days 5 and 10 after ovulation upon the mRNA expression, immunopositive protein expression, and immunohistological localization of IGF2, IGF binding protein 1 (IGFBP1) and matrix metalloproteinases (MMPs) 2 and 9 in the implantation-stage endometrium collected on day 13 after ovulation from fecund cycles of rhesus monkeys. The comparison between isotype-matched IgG (control; nZ8)-and VEGF antibody (VEGF Mab; nZ8)-treated animals revealed higher (P!0.05) IGF2 in lacunar and villous syncytiotrophoblasts, trophoblast cell columns, migrating extravillous trophoblast cells, and endovascular trophoblast cells in control animals, but with no change in the various cell types of maternal endometrium between the two groups. No change in IGFBP1 expression in the endometrium was observed between the two groups. MMPs 2 and 9 were detected in syncytiotrophoblast in lacunae and villi, trophoblast cell columns, and extravillous trophoblast cells in control samples. MMP9 transcript expression in maternal endometrium and its immunopositivity in endometrial stroma and trophoblast cells were lower (P!0.05) with no change in MMP2 level in VEGF Mab-exposed samples compared with those in control samples. A functional network involving VEGF, IGF2, and MMP9 in early placental trophoblast cells and maternal endometrium appears to be important for normal placentation.

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“…The RNA integrity number (RIN) calculated by Agilent's Bioanalyzer software takes the ratio of the ribosomal bands and the complete electrophoretic trace into consideration and has been proposed as a convenient technique for determining the integrity of total RNA [29]. Despite its convenience it has been suggested to use the RIN and the rRNA ratios rather as approximate values and not as accurate measures as they have not been validated thoroughly for total RNA from bacteria and inconsistent results were obtained from mixed RNA samples [21].…”

Section: Resultsmentioning

confidence: 99%

Improved Method for Isolation of Microbial RNA from Biofuel Feedstock for Metatranscriptomics

Piao¹,

Markillie²,

Culley³

et al. 2013

AiM

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Metatranscriptomics-gene express profiling via DNA sequencing-is a powerful tool to identify genes that are actively expressed and might contribute to the phenotype of individual organisms or the phenome (the sum of several phenotypes) of a microbial community. Furthermore, metatranscriptome studies can result in extensive catalogues of genes that encode for enzymes of industrial relevance. In both cases, a major challenge for generating a high quality metatranscriptome is the extreme lability of RNA and its susceptibility to ubiquitous RNAses. The microbial community (the microbiome) of the cow rumen efficiently degrades lignocelullosic biomass, generates significant amounts of methane, a greenhouse gas twenty times more potent than carbon dioxide, and is of general importance for the physiological wellbeing of the host animal. Metatranscriptomes of the rumen microbiome from animals kept under different conditions and from various types of rumen-incubated biomass can be expected to provide new insights into these highly interesting phenotypes and subsequently provide the framework for an enhanced understanding of this socioeconomically important ecosystem. The ability to isolate large amounts of intact RNA will significantly facilitate accurate transcript annotation and expression profiling. Here we report a method that combines mechanical disruption with chemical homogenization of the sample material and consistently yields 1 mg of intact RNA from 1 g of rumen-incubated biofuel feedstock. The yield of total RNA obtained with our method exceeds the RNA yield achieved with previously reported isolation techniques, which renders RNA isolated with the method presented here as an ideal starting material for metatranscriptomic analyses and other molecular biology applications that require significant amounts of starting material.

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The RIN: an RNA integrity number for assigning integrity values to RNA measurements

Cited by 2,045 publications

References 10 publications

De-novo characterization of the soft-shelled turtle Pelodiscus sinensis transcriptome using Illumina RNA-Seq technology

De-novo characterization of the soft-shelled turtle Pelodiscus sinensis transcriptome using Illumina RNA-Seq technology

IGF2, IGF binding protein 1, and matrix metalloproteinases 2 and 9 in implantation-stage endometrium following immunoneutralization of vascular endothelial growth factor in the rhesus monkey

Improved Method for Isolation of Microbial RNA from Biofuel Feedstock for Metatranscriptomics

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