Ribo spia technology

Manufactured by Tecan

Sourced in United States

Ribo-SPIA Technology is a laboratory tool developed by Tecan. It provides a platform for the analysis of protein synthesis and translation processes in biological systems. The core function of this technology is to enable the measurement and quantification of newly synthesized proteins within a sample, without making interpretations or extrapolations about its intended use.

Automatically generated - may contain errors

Lab products found in correlation

Hiseq 2000, by Illumina (2 mentions) Hiseq 2000 platform, by Illumina (1 mentions) Genechip expression analysis, by Thermo Fisher Scientific (1 mentions) Nugen ovation one direct system, by Tecan (1 mentions) Nugen ovation encore biotin module, by Tecan (1 mentions) Ampure xp bead, by Beckman Coulter (1 mentions) Lmd7000 laser microdissection system, by Leica camera (1 mentions) Hiseq 2500, by Illumina (1 mentions) Flow cell, by Illumina (1 mentions) Ovation rna seq system v2 protocol, by Tecan (1 mentions) Hiseq 2500 platform, by Illumina (1 mentions) Allprep dna rna mini kit, by Qiagen (1 mentions) Agilent sureselect human all exon v4 kit, by Agilent Technologies (1 mentions)

6 protocols using ribo spia technology

RNA-Seq Analysis Pipeline for Fusion Transcripts

Cited 3 times

Check if the same lab product or an alternative is used in the 5 most similar protocols

cDNA was synthesized via Ribo-SPIA Technology (NuGEN, San Carlos, CA) per the manufacturer’s instructions. The synthesized cDNA library was sequenced by Illumina’s HiSeq 2000 platform. Raw sequencing data from the Illumina platform were converted to fastq files and aligned to the reference genome (hg19) using the Spliced Transcripts Alignment to a Reference (STAR) algorithm^{44 (link)}. HTSeq-count was then utilized to generate the raw counts for each gene^{45 (link)}. Raw counts were then analyzed by DESeq2 for data processing, normalization, and differential expression analysis according to standard procedures^{46 (link)}. To identify candidate fusion transcripts, we ran three different structural variation (SV) detection algorithms: TopHat-Fusion^{47 (link)}, FusionMap^{48 (link)}, and MapSplice^{49 (link)}. SVs that met the following criteria were considered candidate fusion transcripts: (1) SVs supported consistently by 2 or more algorithms, (2) in-frame fusion transcripts, (3) reads that were not mapped to different transcripts by Blat search, (4) supporting seed reads count ≥4, and (5) junction located at the exon-intron boundaries.

Takahashi K., Wang F., Morita K., Yan Y., Hu P., Zhao P., Zhar A.A., Wu C.J., Gumbs C., Little L., Tippen S., Thornton R., Coyle M., Mendoza M., Thompson E., Zhang J., DiNardo C.D., Jain N., Ravandi F., Cortes J.E., Garcia-Manero G., Kornblau S., Andreeff M., Jabbour E., Bueso-Ramos C., Takaori-Kondo A., Konopleva M., Patel K., Kantarjian H, & Futreal P.A. (2018). Integrative genomic analysis of adult mixed phenotype acute leukemia delineates lineage associated molecular subtypes. Nature Communications, 9, 2670.

+ Open protocol

+ Expand

Transcriptome Amplification and Expression Profiling of Rhesus Macaque

Check if the same lab product or an alternative is used in the 5 most similar protocols

cDNA synthesis and amplification was performed with the NuGEN Ovation One-Direct System (NuGEN, San Carlos, CA, USA). Total RNA was used for cDNA synthesis followed by whole transcriptome amplification by NuGEN's Ribo-SPIA® technology. The amplified single stranded DNA was purified with AMpure XP beads (Beckman, Indianapolis, IN, USA). Qualitative and quantitative analyses were performed on the Bioanalyzer and NanoDrop, respectively. 5 μg of the amplified DNA was used for biotinylation and fragmentation using the NuGEN Ovation Encore Biotin Module (Nugen, San Carlos, CA, USA). All samples were hybridized to Affymetrix GeneChip® Rhesus Macaque Genome Arrays (Affymetrix, Santa Clara, CA, USA). The probe arrays were washed, stained and scanned as described in the Affymetrix GeneChip® Expression Analysis Technical Manual. CEL files were extracted from the raw scanned images using the Affymetrix GeneChip® command console Software. Quality Control metrics were monitored on the Affymetrix Expression console software; discordant arrays were excluded from further downstream analyses.

Tuyishime S., Haut L.H., Kurupati R.K., Billingsley J.M., Carnathan D., Gangahara S., Styles T.M., Xiang Z., Li Y., Zopfs M., Liu Q., Zhou X., Lewis M.G., Amara R.R., Bosinger S., Silvestri G, & Ertl H.C. (2018). Correlates of Protection Against SIVmac251 Infection in Rhesus Macaques Immunized With Chimpanzee-Derived Adenovirus Vectors. EBioMedicine, 31, 25-35.

+ Open protocol

+ Expand

Syncytiotrophoblast RNA-seq from Placenta Tissue

Check if the same lab product or an alternative is used in the 5 most similar protocols

We used a Leica LMD 7000 Laser Microdissection system to collect syncytiotrophoblast from fresh-frozen sectioned tissue. Microdissected material was collected directly into the lysis buffer of the Qiagen RNasy Plus Micro kit, and RNA was extracted subsequently. Two samples were collected from the same placenta. Due to low concentration, the Ovation RNA Amplification System (Ribo-SPIA technology, NuGen) was used to amplify cDNA. Libraries were sequenced using Illumina HiSeq2500, to obtain a minimum of 30 million 75-bp paired-end reads per sample. Reads were aligned using Bowtie, counted and normalized using RNA-eXpress.

Pavličev M., Wagner G.P., Chavan A.R., Owens K., Maziarz J., Dunn-Fletcher C., Kallapur S.G., Muglia L, & Jones H. (2017). Single-cell transcriptomics of the human placenta: inferring the cell communication network of the maternal-fetal interface. Genome Research, 27(3), 349-361.

+ Open protocol

+ Expand

RNA Extraction and Illumina Sequencing

Check if the same lab product or an alternative is used in the 5 most similar protocols

Extracted RNA was converted to cDNA using Ribo-SPIA Technology (NuGEN, San Carlos, CA). The cDNA library was then sequenced on Illumina HiSeq 2000 platform using 76 bp paired-end reads.

Lee W.C., Reuben A., Hu X., McGranahan N., Chen R., Jalali A., Negrao M.V., Hubert S.M., Tang C., Wu C.C., Lucas A.S., Roh W., Suda K., Kim J., Tan A.C., Peng D.H., Lu W., Tang X., Chow C.W., Fujimoto J., Behrens C., Kalhor N., Fukumura K., Coyle M., Thornton R., Gumbs C., Li J., Wu C.J., Little L., Roarty E., Song X., Lee J.J., Sulman E.P., Rao G., Swisher S., Diao L., Wang J., Heymach J.V., Huse J.T., Scheet P., Wistuba I.I., Gibbons D.L., Futreal P.A., Zhang J., Gomez D, & Zhang J. (2020). Multiomics profiling of primary lung cancers and distant metastases reveals immunosuppression as a common characteristic of tumor cells with metastatic plasticity. Genome Biology, 21, 271.

+ Open protocol

+ Expand

RNA-Seq Library Preparation from Biopsy Samples

Check if the same lab product or an alternative is used in the 5 most similar protocols

RNA was extracted from biopsy samples using the Qiagen Allprep DNA/RNA mini kit (Qiagen, Valencia, CA). An Agilent 2100 Bioanalyzer was used to identify samples with RIN ≥ 7. The Ovation RNA-Seq System V2 protocol (NuGEN, San Carlos, CA) was implemented to amplify cDNA from 500 pg of qualified mRNA from each sample. In brief, cDNA amplification was performed using NuGEN’s Ribo-SPIA technology to yield several micrograms of cDNA. The cDNA was then sheared as ~200 bp fragments, end-repaired, followed by A-tailing and adapter ligation reactions. The library was then PCR enriched and purified using the Ampure XP bead size selection method to generate the final product. All libraries were quantified by Caliper and real-time qPCR. The qualified libraries were amplified on cBot to generate clusters on the Illumina flowcell, and sequenced on the Illumina HiSeq 2500 platform, yielding an average of 60.7 million 100-bp paired-end reads per sample.

Ahn R.S., Taravati K., Lai K., Lee K.M., Nititham J., Gupta R., Chang D.S., Arron S.T., Rosenblum M, & Liao W. (2017). Transcriptional landscape of epithelial and immune cell populations revealed through FACS-seq of healthy human skin. Scientific Reports, 7, 1343.

+ Open protocol

+ Expand

Transcriptome and Exome Sequencing of NSCLC

Check if the same lab product or an alternative is used in the 5 most similar protocols

Twelve primary tumor samples were collected from four patients with non-small cell lung cancer (3 regions per tumor) including Adenocarcinoma (n=3) and Squamous Cell Carcinoma (n=1). Matched normal samples were collected from white blood cells (n=3) or adjacent lung tissue (n=1). Informed consent was obtained from all patients. No compensation was provided for the patients. Collection and use of patient samples were approved by the Institutional Review Board of The University of Texas MD Anderson Cancer Center (MDACC). Detailed cohort characteristics including age, gender, and smoking status are given in Sup. Table 3.
Using the Ribo-SPIA Technology (NuGen, San Carlos, CA, USA), we converted the extracted RNA to cDNA libraries, which were then sequenced as 76 bp paired-end reads on the Illumina HiSeq 2000 platform (Illumina, Inc., San Diego, CA, USA). Genomic DNA was extracted and utilized for library preparation for sequencing with the Agilent SureSelect Human All Exon V4 kit, according to the manufacturer’s instructions (Agilent Technologies, Inc., Santa Clara, CA, USA). 76-bp paired-end whole exome sequencing was performed on the Illumina HiSeq 2000 platform with mean target sequencing coverage of 200x (Illumina, Inc., San Diego, CA, USA).

Lu T., Park S., Han Y., Wang Y., Hubert S.M., Futreal P.A., Wistuba I., Heymach J.V., Reuben A., Zhang J, & Wang T. (2022). Netie: Inferring the evolution of neoantigen-T cell interactions in tumors. Nature methods, 19(11), 1480-1489.

+ Open protocol

+ Expand

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Revolutionizing how scientists
search and build protocols!