Log In Sign up
The largest database of trusted experimental protocols

Rta software version 2

Manufactured by Illumina
Visit Supplier

RTA software version 2.4.11 is a core component of Illumina's sequencing systems. Its primary function is to perform real-time analysis of the image data generated during the sequencing process.

Automatically generated - may contain errors

Lab products found in correlation

Hiseq 4000, by Illumina (4 mentions) Qubit fluorometry, by Thermo Fisher Scientific (3 mentions) Truseq rna sample prep kit v2, by Illumina (3 mentions) Nextseq 500, by Illumina (2 mentions) Cbot and hiseq 3000 4000 pe cluster kit, by Illumina (2 mentions) Rneasy plus mini kit, by Qiagen (2 mentions) Truseq stranded mrna reagents, by Illumina (1 mentions) Rneasy micro kit, by Qiagen (1 mentions) Chloroform, by Merck Group (1 mentions) Truseq stranded mrna sample preparation kit, by Illumina (1 mentions) Rnalater, by Thermo Fisher Scientific (1 mentions) Hiseq 3000 4000 pe cluster kit, by Illumina (1 mentions) Bioanalyzer dna 1000 chip, by Thermo Fisher Scientific (1 mentions) Rneasy kit, by Qiagen (1 mentions)

6 protocols using rta software version 2

1

Illumina NextSeq 500 RNA Sequencing Protocol

Check if the same lab product or an alternative is used in the 5 most similar protocols
Libraries were prepared using TruSeq stranded RNA reagents (Illumina, USA) according to manufacturer’s instructions, using 500 ng of total RNA input per sample with dual indexing to enable all libraries to be sequenced in the same run. Pooled libraries were sequenced on four runs of an Illumina NextSeq 500 instrument with 75 bp single end reads. Image analysis and base calling were performed using Illumina’s RTA software version 2.4.11 and bcl2fastq version 2.18.0.12. Reads were filtered to remove those with low base call quality using Illumina’s default chastity criteria. Raw sequence data were deposited in Sequence Read Archive under Bioproject number PRJNA437839.
Santoro F., Pettini E., Kazmin D., Ciabattini A., Fiorino F., Gilfillan G.D., Evenroed I.M., Andersen P., Pozzi G, & Medaglini D. (2018). Transcriptomics of the Vaccine Immune Response: Priming With Adjuvant Modulates Recall Innate Responses After Boosting. Frontiers in Immunology, 9, 1248.
+ Open protocol
+ Expand
2

RNA Isolation and Sequencing of Chalimus Larvae

Check if the same lab product or an alternative is used in the 5 most similar protocols
RNA was isolated as described before [37 (link)]. In brief, pools of four or five chalimus larvae were homogenized in TRI reagent and mixed with chloroform (both Merck, Darmstadt, Germany). The upper aqueous phase was aspirated and further purified using an RNeasy Micro Kit (Qiagen, Hilden, Germany) for RNA isolation according to the manufacturers’ instructions. RNA was stored at − 80 °C until use. Library preparation and RNA-sequencing were conducted by the Norwegian Sequencing Centre, Oslo, as previously described [27 (link)]. Briefly, sequencing libraries were prepared from 0.5 µg total RNA using the TruSeq stranded mRNA reagents (Illumina, San Diego, USA). Indexed libraries were blended into a single pool and sequenced during three runs of a NextSeq 500 instrument (Illumina) using 76-bp single end reads. Image analysis and base calling were performed using Illumina’s RTA software version 2.4.11, and data were converted to FASTQ format using bcl2fastq version 2.17.1.14. Raw sequencing data were deposited in the NCBI database under BioProject ID PRJNA577842.
Heggland E.I., Dondrup M., Nilsen F, & Eichner C. (2020). Host gill attachment causes blood-feeding by the salmon louse (Lepeophtheirus salmonis) chalimus larvae and alters parasite development and transcriptome. Parasites & Vectors, 13, 225.
+ Open protocol
+ Expand
3

Transcriptomic Analysis of FTZ-F1 Knockdown

Check if the same lab product or an alternative is used in the 5 most similar protocols
Nauplii I larvae originating from the same pair of eggstrings were divided into three groups and treated with 2500 ng dsRNA of either αFTZ-F1, βFTZ-F1 or CPY185 (control). About 50 larvae from each group were transferred to RNAlater™ (Ambion) 48 hours after molting from nauplius I to nauplius II, and the remaining larvae were left to molt again and develop to copepodids. This experiment was repeated three times, producing three biological parallels per dsRNA treatment. Total RNA extracted from dsRNA treated larvae were sequenced at the Genomics Core Facility, University of Bergen. Sequencing libraries were prepared from 400 ng total RNA using Illumina® TruSeq® mRNA Stranded Sample Preparation kit. Samples were barcoded, pooled together and sequenced in a single lane using the Illumina HiSeq4000 (Illumina, Inc., San Diego, CA, USA), producing 2x75 base pair (bp) paired end reads. Image analysis and base calling were performed using Illumina’s RTA software version 2.4.11, and the data was converted to fastQ format using bcl2fastq version 2.1.7.1.14.
Brunet J., Eichner C, & Male R. (2021). The FTZ-F1 gene encodes two functionally distinct nuclear receptor isoforms in the ectoparasitic copepod salmon louse (Lepeophtheirus salmonis). PLoS ONE, 16(5), e0251575.
+ Open protocol
+ Expand
4

RNA-seq Analysis of Mouse Alveolar Macrophages

Cited 1 time
Check if the same lab product or an alternative is used in the 5 most similar protocols
Total RNA from in vitro cultured AMs was extracted using RNeasy Plus Mini Kit (QIAGEN) following the manufacture’s protocol. Two pools per genotype were used for RNA-seq. After quality control, high quality (Agilent Bioanalyzer RIN > 7.0) total RNA was used to generate the RNA sequencing library. cDNA synthesis, end-repair, A-base addition, and ligation of the Illumina indexed adapters were performed according to the TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego, CA). The concentration and size distribution of the completed libraries was determined using an Agilent Bioanalyzer DNA 1000 chip (Santa Clara, CA) and Qubit fluorometry (Invitrogen, Carlsbad, CA). Paired-end libraries were sequenced on an Illumina HiSeq 4000 following Illumina’s standard protocol using the Illumina cBot and HiSeq 3000/4000 PE Cluster Kit. Base-calling was performed using Illumina’s RTA software (version 2.5.2). Paired-end RNA-seq reads were aligned to the mouse reference genome (GRCm38/mm10) using Bowtie (v2.3.4). Pre- and post-alignment quality controls, gene level raw read count and normalized read count (i.e., FPKM) were performed using RSeQC package (v2.3.6) with NCBI mouse RefSeq gene model. Differential expression for each gene between various groups specified in the text was identified by Cuffdiff (Trapnell et al., 2010 (link)).
Zhu B., Wu Y., Huang S., Zhang R., Son Y.M., Li C., Cheon I.S., Gao X., Wang M., Chen Y., Zhou X., Nguyen Q., Phan A.T., Behl S., Taketo M.M., Mack M., Shapiro V.S., Zeng H., Ebihara H., Mullon J.J., Edell E.S., Reisenauer J.S., Demirel N., Kern R.M., Chakraborty R., Cui W., Kaplan M.H., Zhou X., Goldrath A.W, & Sun J. (2021). Uncoupling of macrophage inflammation from self-renewal modulates host recovery from respiratory viral infection. Immunity, 54(6), 1200-1218.e9.
+ Open protocol
+ Expand
5

RNA-Seq Protocol for Alveolar Macrophages

Cited 1 time
Check if the same lab product or an alternative is used in the 5 most similar protocols
Total RNA from in vitro cultured AMs was extracted using RNeasy Plus Mini Kit (Qiagen) following the manufacture’s protocol. Two pools per genotype were used for RNA-seq. After quality control, high quality (Agilent Bioanalyzer RIN >7.0) total RNA was used to generate the RNA sequencing library. cDNA synthesis, end-repair, A-base addition, and ligation of the Illumina indexed adapters were performed according to the TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego, CA). The concentration and size distribution of the completed libraries was determined using an Agilent Bioanalyzer DNA 1000 chip (Santa Clara, CA) and Qubit fluorometry (Invitrogen, Carlsbad, CA). Paired-end libraries were sequenced on an Illumina HiSeq 4000 following Illumina’s standard protocol using the Illumina cBot and HiSeq 3000/4000 PE Cluster Kit. Base-calling was performed using Illumina’s RTA software (version 2.5.2). Paired-end RNA-seq reads were aligned to the mouse reference genome (GRCm38/mm10) using Bowtie (v2.3.4). Pre- and post-alignment quality controls, gene level raw read count and normalized read count (i.e. FPKM) were performed using RSeQC package (v2.3.6) with NCBI mouse RefSeq gene model. Differential expression for each gene between various groups specified in the text was identified by Cuffdiff (Trapnell et al., 2010 (link)).
Zhu B., Wu Y., Huang S., Zhang R., Son Y.M., Li C., Cheon I.S., Gao X., Wang M., Chen Y., Zhou X., Nguyen Q., Phan A.T., Behl S., Taketo M.M., Mack M., Shapiro V.S., Zeng H., Ebihara H., Mullon J.J., Edell E.S., Reisenauer J.S., Demirel N., Kern R.M., Chakraborty R., Cui W., Kaplan M.H., Zhou X., Goldrath A.W, & Sun J. (2021). Uncoupling of macrophage inflammation from self-renewal modulates host recovery from respiratory viral infection. Immunity, 54(6), 1200-1218.e9.
+ Open protocol
+ Expand
6

RNA-seq Analysis of CD8+ T Cells

Check if the same lab product or an alternative is used in the 5 most similar protocols
RNA from Sorted CD8+ T cells was extracted using an RNeasy kit (Qiagen) following the manufacturer’s instructions. After quality control, High quality total RNA was used to generate the RNA sequencing library. cDNA synthesis, end-repair, A-base addition, and ligation of the Illumina indexed adapters were performed according to the TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego, CA). The concentration and size distribution of the completed libraries was determined using an Agilent Bioanalyzer DNA 1000 chip (Santa Clara, CA) and Qubit fluorometry (Invitrogen, Carlsbad, CA). Paired-end libraries were sequenced on an Illumina HiSeq 4000 following Illumina’s standard protocol using the Illumina cBot and HiSeq 3000/4000 PE Cluster Kit. Base-calling was performed using Illumina’s RTA software (version 2.5.2). Paired-end RNA-seq reads were aligned to the mouse reference genome (GRCm38/mm10) using RNA-seq spliced read mapper Tophat2 (v2.1.1). Pre- and post-alignment quality controls, gene level raw read count and ormalized read count (i.e. FPKM) were performed using RSeQC package (v2.3.6) with NCBI mouse RefSeq gene model. RNA-seq data were deposited in GEO database (GEO: GSE135278).
Li C., Zhu B., Son Y., Wang Z., Jiang L., Xiang M., Ye Z., Beckermann K.E., Wu Y., Jenkins J., Siska P.J., Vincent B.G., Prakash Y.S., Peikert T., Edelson B.T., Taneja R., Kaplan M.H., Rathmell J.C., Dong H., Hitosugi T, & Sun J. (2019). The transcription factor Bhlhe40 programs mitochondrial regulation of resident CD8+ T cell fitness and functionality. Immunity, 51(3), 491-507.e7.
+ 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?

Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required

Sign up now

Revolutionizing how scientists
search and build protocols!