Ribo zero rrna kit

Manufactured by Illumina

Sourced in United States

The Ribo-Zero rRNA kit is a laboratory product designed for the depletion of ribosomal RNA (rRNA) from total RNA samples. It enables the enrichment of non-rRNA species, such as messenger RNA (mRNA) and other functional RNA molecules, to facilitate downstream applications, such as RNA sequencing and analysis.

Automatically generated - may contain errors

Lab products found in correlation

Rneasy mini kit, by Qiagen (4 mentions) Dneasy ultraclean microbial kit, by Qiagen (2 mentions) Nanodrop system, by Thermo Fisher Scientific (2 mentions) Qubit fluorometer microplate reader, by Thermo Fisher Scientific (2 mentions) Nextseq 500, by Illumina (2 mentions) Truseq stranded total rna library prep kit, by Illumina (2 mentions) Kapa library quantification kit for libraries, by Illumina (2 mentions) Dna high sensitivity hs kit, by Agilent Technologies (2 mentions) Agilent 2100 bioanalyzer, by Agilent Technologies (2 mentions) Turbo dna free kit, by Thermo Fisher Scientific (2 mentions) 2100 bioanalyzer, by Agilent Technologies (1 mentions) 2100 bioanalyzer, by Illumina (1 mentions) Hiseq 4000 platform, by Illumina (1 mentions) Hiseq 2500 platform, by Illumina (1 mentions) Qubit 2.0 fluorometer, by Thermo Fisher Scientific (1 mentions)

Spelling variants of this product

Ribo-Zero kit (234 citations) Ribo-Zero (187 citations) Ribo-Zero human and bacterial rRNA removal kits (2 citations) Ribo-Zero rRNA removal kits for gram-negative bacteria (2 citations)

6 protocols using ribo zero rrna kit

DNA and RNA Extraction Protocol

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The DNA extractions from the samples were performed using DNeasy Ultraclean microbial kits (Qiagen, Germany) according to the manufacturer’s protocol. The quality of DNA and its concentrations were assessed using a NanoDrop system and a Qubit Fluorometer/microplate reader (Thermo Fisher Scientific, USA).
The RNA extractions from the samples were performed using the RNeasy mini kit (Qiagen, Germany) according to the manufacturer’s protocol. Ribosomal RNA was removed from the total RNA using the Illumina Ribo-Zero rRNA kit (Illumina, USA) according to the manufacturer’s protocol.

Saenz C., Fang Q., Gnanasekaran T., Trammell S.A., Buijink J.A., Pisano P., Wierer M., Moens F., Lengger B., Brejnrod A, & Arumugam M. (2023). Clostridium scindens secretome suppresses virulence gene expression of Clostridioides difficile in a bile acid-independent manner. Microbiology Spectrum, 11(5), e03933-22.

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DNA and RNA Extraction Protocol

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Transcriptome Sequencing of Total RNA

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Total RNA was isolated using RNeasy Mini Kit (Qiagen; Cat#: 74104) followed by Turbo DNA-free Kit (Thermo Fisher; Cat#: AM1907). To construct libraries, 1 μg of high-quality total RNA (RIN > 9.9) was processed with Truseq Stranded Total RNA Library Prep Kit (Illumina; Cat#: 20020596) according to the manufacturer's instructions. Briefly, after removal of ribosomal RNA using Ribo-zero rRNA Kit (Illumina; Cat#: 20037135), confirmed by quality control on the Agilent 2100 Bioanalyzer, total RNA molecules were fragmented and reverse-transcribed using random primers. Replacement of dTTP by dUTP during the second strand synthesis permitted to achieve strand specificity. The addition of a single A base to the cDNA was followed by ligation of adapters. Libraries were quantified by qPCR using the KAPA Library Quantification Kit for Illumina Libraries (KapaBiosystems; Cat#: KR0405) and library profiles were assessed using the DNA High Sensitivity HS Kit (Agilent; Cat#: 5067-4626) on an Agilent Bioanalyzer 2100. Libraries were sequenced on an Illumina Nextseq 500 in a paired-end mode in three independent biological replicates at Platform GENOM’IC - Institute Cochin. Demultiplexing and quality of sequences were performed with the Aozan software v2.2.1.

Zakharova V.V., Magnitov M.D., Del Maestro L., Ulianov S.V., Glentis A., Uyanik B., Williart A., Karpukhina A., Demidov O., Joliot V., Vassetzky Y.S., Mège R.M., Piel M., Razin S.V, & Ait-Si-Ali S. (2022). SETDB1 fuels the lung cancer phenotype by modulating epigenome, 3D genome organization and chromatin mechanical properties. Nucleic Acids Research, 50(8), 4389-4413.

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RNA Sequencing Library Preparation

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Total RNA was isolated using RNeasy Mini Kit (Qiagen; Cat#: 74104) followed by Turbo DNAfree Kit (Thermo Fisher; Cat#: AM1907). To construct libraries, 1 µg of high-quality total RNA (RIN > 9.9) was processed with Truseq Stranded Total RNA Library Prep Kit (Illumina; Cat#: 20020596) according to the manufacturer's instructions. Briefly, after removal of ribosomal RNA using Ribo-zero rRNA Kit (Illumina; Cat#: 20037135), confirmed by quality control on the Agilent 2100 Bioanalyzer, total RNA molecules were fragmented and reverse-transcribed using random primers. Replacement of dTTP by dUTP during the second strand synthesis permitted to achieve strand specificity. The addition of a single A base to the cDNA was followed by ligation of adapters. Libraries were quantified by qPCR using the KAPA Library Quantification Kit for Illumina Libraries (KapaBiosystems; Cat#: KR0405) and library profiles were assessed using the DNA High Sensitivity HS Kit (Agilent; Cat#: 5067-4626) on an Agilent Bioanalyzer 2100.
Libraries were sequenced on an Illumina Nextseq 500 in a paired-end mode in three independent biological replicates at Platform GENOM'IC -Institute Cochin. Demultiplexing and quality of sequences were performed with the Aozan software v2.2.1.

Zakharova V., Magnitov M., Del-Maestro L., Ulianov S.V., Glentis A., Ulyanik B., Williart A., Karpukhina A., Demidov O.N., Joliot V., Vassetzky Y., Mège R., Piel M., Razin S.V., & Ait‐Si‐Ali S. (2021). SETDB1 Fuels the Lung Cancer Phenotype by Modulating Epigenome, 3D Genome Organization and Chromatin Mechanical Properties.

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Comprehensive Transcriptomic Profiling Protocol

Cited 1 time

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RNA extraction and purity, library construction, and Illumina sequencing were performed according to Lv et al. [33 (link)]. Briefly, after total RNA extraction, rRNAs were removed using an Epicenter Ribo-Zero rRNA Kit (Epicenter, USA, cat: MRZSR116), and 1 µg of rRNA-depleted RNA per sample was used to generate sequencing libraries according to the manual provided by Gene Denovo Biotechnology Co. (Guangzhou, China). The qualified libraries were then constructed and sequenced using an Illumina HiSeq 4000 platform. The 12 gene expression libraries were named HP-NR-1, HP-NR-2, HP-NR-3; LP-NR-1, LP-NR-2, LP-NR-3; HP-BR-1, HP-BR-2, HP-BR-3; LP-BR-1, LP-BR-2, and LP-BR-3. The lncRNAs, mRNAs, miRNAs and circRNAs were sequenced simultaneously using the same samples and corresponding published results [32 , 33 (link), 48 (link)].

Zhang J., Xu H., Yang Y., Zhang X., Huang Z, & Zhang D. (2021). Genome-wide analysis of long non-coding RNAs (lncRNAs) in two contrasting soybean genotypes subjected to phosphate starvation. BMC Genomics, 22, 433.

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Strand-Specific RNA-seq Library Preparation

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For the preparation of mRNA for RNA-seq, the Ribo-Zero-rRNA kit (Epicentre, USA) was initially used to remove rRNA from the RNA samples. The final concentration of RNA samples was determined with a Qubit 2.0 Fluorometer (Thermo Fisher, USA). The VAHTS Stranded mRNA-seq Library Prep Kit for Illumina (Vazyme, China) was used to construct strand-specific RNA-seq libraries, and sequencing was conducted on an Illumina HiSeq 2500 platform, yielding the paired-end reads. Adapter sequences and low-quality bases (PHRED quality scores ≤ 5) were trimmed with the Trimmomatic package (Bolger et al. 2014 ) using the default parameters and reads smaller than 35 bp were discarded. The RNA-seq data processing procedures and statistical analysis were performed (Tjaden 2015 ).

Mao Q., Jiang J., Wu X., Xu R., Ma Y., Zhang Y., Shao S, & Wang Q. (2022). Coordinate regulation of carbohydrate metabolism and virulence by PtsH in pathogen Edwardsiella piscicida. Applied Microbiology and Biotechnology, 106(5-6), 2063-2077.

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