Rta version 1

Manufactured by Illumina

RTA version 1.17.21.3 is a software component used in Illumina's sequencing instruments. It is responsible for the real-time analysis of data generated during the sequencing process.

Automatically generated - may contain errors

Lab products found in correlation

Truseq sbs sequencing kit version 3, by Illumina (13 mentions) Hiseq 2000, by Illumina (11 mentions) Truseq rna sample prep kit v2, by Illumina (8 mentions) Cbot and cbot paired end cluster kit version 3, by Illumina (8 mentions) Hiseq 2500, by Illumina (7 mentions) Truseq rapid sbs sequencing kit version 1, by Illumina (3 mentions) Ribo zero gold, by Illumina (3 mentions) Truseq stranded total rna library prep kit, by Illumina (3 mentions) Agilent bioanalyzer, by Agilent Technologies (3 mentions) Hiseq 2500 or 4000, by Illumina (3 mentions) Ampure xp bead, by Beckman Coulter (3 mentions) Truseq rna access library prep kit, by Illumina (2 mentions) Qiacube system, by Qiagen (2 mentions) Hiseq sbs kit v4, by Illumina (2 mentions) Fragment analyzer, by Agilent Technologies (2 mentions) Truseq polya stranded mrna library prep kit highthroughput, by Illumina (2 mentions) Bioanalyzer dna 1000 chip, by Agilent Technologies (2 mentions) Truseq rna sample prep kit, by Illumina (2 mentions) Sureselect human all exon 71 mb v6 kit, by Agilent Technologies (2 mentions) Cbot and hiseq paired end cluster kit version 3, by Illumina (2 mentions)

Spelling variants of this product

RTA 1.18.64 (17 citations) Real-Time Analysis version 1.8.70 (RTA v1.8.70). (8 citations) Primary Analysis version RTA 1.18.64 (4 citations)

26 protocols using rta version 1

Bulk RNA Sequencing of Blood and Fibroblasts

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

Sequencing was conducted on blood for 46 patients and cultured fibroblasts for 1 patient due to sample availability. Blood-derived RNA was obtained by collecting peripheral whole blood in PAXgene blood RNA tubes and using the QIAcube system (Qiagen) according to the manufacturer’s protocol for RNA extraction. RNA was isolated from fibroblasts as previously described [34 (link)].
Sequencing libraries were prepared with either the TruSeq RNA Sample Prep Kit v2 or the TruSeq RNA Access Library Prep Kit (Illumina, San Diego, CA). Paired-end 101-basepair reads were sequenced on an Illumina HiSeq 2500 using the TruSeq Rapid SBS sequencing kit version 1 and HCS version 2.0.12.0 data collection software. A median of approximately 200 million reads was generated per individual. Base calling was performed using Illumina’s RTA version 1.17.21.3.

Oliver G.R., Tang X., Schultz-Rogers L.E., Vidal-Folch N., Jenkinson W.G., Schwab T.L., Gaonkar K., Cousin M.A., Nair A., Basu S., Chanana P., Oglesbee D, & Klee E.W. (2019). A tailored approach to fusion transcript identification increases diagnosis of rare inherited disease. PLoS ONE, 14(10), e0223337.

+ Open protocol

+ Expand

RNA-Seq Data Analysis Pipeline

Cited 1 time

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

Total RNA was isolated as described above and RNA libraries were prepared according to the manufacturer's instructions for the TruSeq RNA Sample Prep Kit v2 (Illumina). Libraries were loaded onto paired end flow cells following the standard protocol for the Illumina cBot and cBot Paired end cluster kit version 3. Flow cells were sequenced as 51 × 2 paired end reads on an Illumina HiSeq 2000 using TruSeq SBS sequencing kit version 3 and HCS v2.0.12 data collection software. Base-calling was performed using Illumina's RTA version 1.17.21.3. The RNA-Seq data was analyzed using MAP-RSeq v.1.2.1 [65 (link)], the Mayo Bioinformatics Core pipeline. MAP-RSeq consists of alignment with TopHat 2.0.6 [66 (link)] against the hg19 genome build and gene counts with the HTSeq software 0.5.3p9 (http://www.huber.embl.de/users/anders/HTSeq/doc/overview.html) using gene annotation files obtained from Illumina (http://cufflinks.cbcb.umd.edu/igenomes.html). Normalization and differential expression analysis were performed using edgeR 2.6.2 [67 (link)].

Lalia A.Z., Dasari S., Robinson M.M., Abid H., Morse D.M., Klaus K.A, & Lanza I.R. (2017). Influence of omega-3 fatty acids on skeletal muscle protein metabolism and mitochondrial bioenergetics in older adults. Aging (Albany NY), 9(4), 1096-1115.

+ Open protocol

+ Expand

RNA Sequencing Library Preparation and Illumina Sequencing

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

RNA libraries were prepared according to the manufacturer’s instructions for the TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego, CA). Then the libraries were loaded onto paired end flow cells following Illumina’s standard protocol using the Illumina cBot and cBot Paired end cluster kit version 3. The flow cells were sequenced on an Illumina HiSeq 2000 using TruSeq SBS sequencing kit version 3 and HCS v2.0.12 data collection software. Base-calling were performed using Illumina’s RTA version 1.17.21.3.

Holcomb M., Ding Y.H., Dai D., McDonald R.J., McDonald J.S., Kallmes D.F, & Kadirvel R. (2015). RNA-Sequencing Analysis of Messenger RNA/MicroRNA in a Rabbit Aneurysm Model Identifies Pathways and Genes of Interest. AJNR: American Journal of Neuroradiology, 36(9), 1710-1715.

+ Open protocol

+ Expand

Sequencing miRNA Libraries Using Illumina

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

miRNA libraries will be prepared according to manufacturer’s instructions for the NEBNext Multiplex Small RNA Kit (New England Biolabs; Ipswich, MA). Then the libraries were loaded onto paired end flow cells following Illumina’s standard protocol using the Illumina cBot and cBot Paired end cluster kit version 3. The flow cells were sequenced on an Illumina HiSeq 2000 using TruSeq SBS sequencing kit version 3 and HCS v2.0.12 data collection software. Base-calling was performed using Illumina’s RTA version 1.17.21.3.

+ Open protocol

+ Expand

High-Resolution RNA-Seq of Adipose-Derived MSCs

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

High‐resolution RNA‐sequencing (RNA‐seq) was performed using three distinct adipose tissue‐derived MSCs from different human donors 9. MSC cultures were each treated in triplicate for 24 hours with or without Cytochalasin D. The resulting biological triplicates for each of the three donors were pooled prior to RNA‐seq to yield technically robust datasets. RNA‐seq analysis of MSCs was performed as described previously 9, 18 with oligo dT purified mRNA and indexed cDNAs (standard TruSeq Kits 12‐Set A and 12‐Set B) on the Illumina platform (Illumina's RTA version 1.17.21.3). Raw reads were mapped using a well‐established pipeline (Bioinformatics Core standard tool) that includes analysis using the MAPRSeq v.1.2.1 system, alignment with TopHat 2.0.6, gene counting with the HTSeq application, as well as normalization and expression analysis using edgeR. Gene expression is expressed in reads per kilobase pair per million mapped reads (RPKM). The sequencing data are available at Gene Expression Omnibus accession number GSE96788.

Samsonraj R.M., Dudakovic A., Manzar B., Sen B., Dietz A.B., Cool S.M., Rubin J, & van Wijnen A.J. (2017). Osteogenic Stimulation of Human Adipose‐Derived Mesenchymal Stem Cells Using a Fungal Metabolite That Suppresses the Polycomb Group Protein EZH2. Stem Cells Translational Medicine, 7(2), 197-209.

+ Open protocol

+ Expand

Validating Multiple Myeloma Cell Lines

Cited 1 time

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

Data generated from RNA-Seq was used to validate the MM.1S, OPM-2, and RPMI-8226 cells. Base-calling and variant determination was performed using Illumina’s RTA version 1.17.21.3, and the MAPRSeq bioinformatics pipeline (http://bioinformaticstools.mayo.edu/research/maprseq) as described (23 (link)). Variants were compared to RNA-Seq variants present in the Cancer Cell Line Encyclopedia (portals.broadinstitute.org/ccle; (25 )) utilizing publicly available tools from Galaxy (use.galaxy.org). Known translocations were confirmed using gene fusion predictions resulting from the MAPRSeq pipeline, and also compared against CCLE gene fusion predictions. 3T3-L1 cells were from ATCC (www.atcc.org). 5TGM1 cells have not been validated at this time.

Fairfield H., Dudakovic A., Khatib C.M., Farrell M., Costa S., Falank C., Hinge M., Murphy C.S., DeMambro V., Pettitt J.A., Lary C.W., Driscoll H.E., McDonald M.M., Kassem M., Rosen C., Andersen T.L., van Wijnen A.J., Jafari A, & Reagan M.R. (2020). Myeloma-modified adipocytes exhibit metabolic dysfunction and a senescence-associated secretory phenotype (SASP). Cancer research, 81(3), 634-647.

+ Open protocol

+ Expand

Whole Blood RNA Sequencing Protocol

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

Sequencing was conducted on blood for 128 individuals. Blood-derived RNA was obtained by collecting peripheral whole blood in PAXgene blood RNA tubes and using the QIAcube system (Qiagen) according to the manufacturer’s protocol for RNA extraction.
Sequencing libraries were prepared with the TruSeq RNA Access Library Prep Kit (Illumina, San Diego, CA). Paired-end 101-basepair reads were sequenced on an Illumina HiSeq 2500 using the TruSeq Rapid SBS sequencing kit version 1 and HCS version 2.0.12.0 data collection software. A median of approximately 200 million reads was generated per individual. Base calling was performed using Illumina’s RTA version 1.17.21.3.

Jenkinson G., Li Y.I., Basu S., Cousin M.A., Oliver G.R, & Klee E.W. (2020). LeafCutterMD: an algorithm for outlier splicing detection in rare diseases. Bioinformatics, 36(17), 4609-4615.

+ Open protocol

+ Expand

Whole Blood RNA Sequencing Protocol

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

Proband RNA was isolated from peripheral whole blood and a sequencing library was prepared with the TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA). The flow cells were sequenced as 100‐basepair paired‐end reads on an Illumina HiSeq 2500 using TruSeq Rapid SBS sequencing kit version 1 and HCS version 2.0.12.0 data collection software. Base calling was performed using Illumina's RTA version 1.17.21.3.

Oliver G.R., Blackburn P.R., Ellingson M.S., Conboy E., Pinto e Vairo F., Webley M., Thorland E., Ferber M., Van Hul E., van der Werf I.M., Wuyts W., Babovic‐Vuksanovic D, & Klee E.W. (2019). RNA‐Seq detects a SAMD12‐EXT1 fusion transcript and leads to the discovery of an EXT1 deletion in a child with multiple osteochondromas. Molecular Genetics & Genomic Medicine, 7(3), e00560.

+ Open protocol

+ Expand

RNA-seq Library Preparation and Sequencing

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

RNA libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego, CA) according to the manufacturer's instructions. One sample failed library prep and was excluded from the study. The remaining 493 libraries (19 from patients with cryoprostatectomy and 474 from patients with radical prostatectomy) were loaded onto flow cells at concentrations of 8–10 pM to generate cluster densities of 700,000 mm² following Illumina's standard protocol using the Illumina cBot and cBot Paired-End Cluster Kit Version 3. The flow cells were run as 51 paired-end reads on an Illumina HiSeq 2000 using TruSeq SBS sequencing kit version 3 and HCS v2.0.12 data collection software. Base calling was performed using Illumina's RTA version 1.17.21.3. A minimum of 50 million total reads per sample was required for analysis. A total of 234 samples with <50 million total reads were re-sequenced and if no quality issues were identified with the individual runs, BAM files were merged.

Thibodeau S.N., French A.J., McDonnell S.K., Cheville J., Middha S., Tillmans L., Riska S., Baheti S., Larson M.C., Fogarty Z., Zhang Y., Larson N., Nair A., O'Brien D., Wang L, & Schaid D.J. (2015). Identification of candidate genes for prostate cancer-risk SNPs utilizing a normal prostate tissue eQTL data set. Nature Communications, 6, 8653.

+ Open protocol

+ Expand

TruSeq RNA Library Preparation

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

RNA libraries were prepared according to the manufacturer’s instructions for the TruSeq RNA Sample Prep Kit v2 (Illumina, CA). Then the libraries were loaded onto paired end flow cells following Illumina’s standard protocol using the Illumina cBot and cBot Paired end cluster kit version 3 and HCS v2.0.12 data collection software. Base calling were performed using Illumina’s RTA version 1.17.21.3.

Rouchaud A., Johnson C., Thielen E., Schroeder D., Ding Y.H., Dai D., Brinjikji W., Cebral J., Kallmes D.F, & Kadirvel R. (2016). Differential Gene Expression in Coiled versus Flow-Diverter-Treated Aneurysms: RNA Sequencing Analysis in a Rabbit Aneurysm Model. AJNR: American Journal of Neuroradiology, 37(6), 1114-1121.

+ 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!