Hiseq control software rta 2

Manufactured by Illumina

The HiSeq Control Software (HCS) + RTA 2.7 is a software package used to control and manage the operation of Illumina HiSeq sequencing instruments. The core function of this software is to provide the necessary tools and interfaces for users to configure, monitor, and operate the HiSeq system during the sequencing process. The HCS + RTA 2.7 software enables users to set up run parameters, initiate sequencing runs, and process the generated sequencing data.

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Lab products found in correlation

Gf 1 total rna extraction kit, by Vivantis Technologies (1 mentions) Novaseq 6000 system, by Illumina (1 mentions) Truseq stranded mrna lt sample prep kit, by Illumina (1 mentions) Agilent 2100 bioanalyzer, by Agilent Technologies (1 mentions) Vahts universal dna library prep kit, by Illumina (1 mentions)

2 protocols using hiseq control software rta 2

Transcriptome Analysis via Illumina RNA-Seq

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Total RNA samples were extracted and subjected to DNase treatment and RNA cleanup using a GF-1 Total RNA Extraction Kit (Vivantis, Malaysia) according to the manufacturer’s protocol. Three replicates of total RNA samples were used for transcriptome analysis. The integrity of the RNA samples (RIN) was evaluated on an RNA 6000 Nano LapChiprun on Agilent2100 Bioanalyzer (Agilent Technologies, Germany). Samples with a RIN > 8.8 were used in RNA-seq library preparation. One μg of total RNAs was used to generate a sequencing library using an Illumina TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) following the manufacturer’s instructions. RNA-seq libraries were sequenced by an Illumina NovaSeq 6000 System according to the manufacturer’s instructions. Sequencing was carried out using a 2 × 100 bp paired-end (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS) + RTA 2.7 (Illumina). Quality control filtering and 3′ end trimming were analyzed using the FASTX-toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html, released date 5 January 2014) and Trimmomatic software (version 0.36) [36 (link)], respectively.

Sreeratree J., Butsayawarapat P., Chaisan T., Somta P, & Juntawong P. (2022). RNA-Seq Reveals Waterlogging-Triggered Root Plasticity in Mungbean Associated with Ethylene and Jasmonic Acid Signal Integrators for Root Regeneration. Plants, 11(7), 930.

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Illumina-based Library Preparation and Sequencing

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Next-generation sequencing library preparations were constructed following the manufacturer's protocol (VAHTS Universal DNA Library Prep Kit for Illumina), as described previously (5 (link)). Then, libraries with different indexes were multiplexed and loaded on an Illumina HiSeq instrument according to the manufacturer's instructions (Illumina, San Diego, CA, USA). Sequencing was carried out using a 2 × 150 paired-end configuration; image analysis and base calling were conducted by HiSeq Control Software (HCS) + RTA 2.7 (Illumina) on a HiSeq instrument. For paired-end sequencing results, read 1 and read 2 were merged to generate a complete sequence according to their overlapping regions, and a file in FASTA (fa) format was generated. Data were split according to their barcodes. The merged sequences were aligned to the reference sequence by using BWA (version 0.7.12) software. Examined target sites that mapped with ∼100 000 independent reads were selected, and obvious base substitutions were observed at only the targeted base editing sites. Base substitution frequencies were calculated by dividing the base substitution read number by the total read number.

Zhao D., Jiang G., Li J., Chen X., Li S., Wang J., Zhou Z., Pu S., Dai Z., Ma Y., Bi C, & Zhang X. (2022). Imperfect guide-RNA (igRNA) enables CRISPR single-base editing with ABE and CBE. Nucleic Acids Research, 50(7), 4161-4170.

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