Log In Sign up
The largest database of trusted experimental protocols

Ribozero rrna depletion

Manufactured by Illumina
Visit Supplier
Sourced in Germany

The RiboZero rRNA depletion kit is a laboratory tool designed to selectively remove ribosomal RNA (rRNA) from total RNA samples. Its core function is to facilitate the enrichment of non-ribosomal RNA molecules, such as messenger RNA (mRNA), for downstream applications like RNA sequencing.

Automatically generated - may contain errors

Lab products found in correlation

Ercc spike in mix, by Thermo Fisher Scientific (3 mentions) Truseq stranded total rna sequencing kit, by Illumina (3 mentions) Ampure xp bead, by Beckman Coulter (3 mentions) Hiseq 4000, by Illumina (2 mentions) Tapestation, by Agilent Technologies (2 mentions) Hiseq 2500, by Illumina (2 mentions) Rneasy purification kit, by Qiagen (1 mentions) Hiseq 1500, by Illumina (1 mentions) Agilent bioanalyzer rna pico chip, by Agilent Technologies (1 mentions) Ovation rna seq system v2, by Tecan (1 mentions) Qubit 3, by Thermo Fisher Scientific (1 mentions)

6 protocols using ribozero rrna depletion

1

Bulk RNA-seq of Isolated Cell Types

Check if the same lab product or an alternative is used in the 5 most similar protocols
Isolated SG, SC, and RS cells were counted, and 1 × 10 ^ 6 cells were resuspended in 1 mL of Trizol and spiked with 1 uL of 1:10 diluted ERCC Spike-in Mix (Invitrogen). RNA was purified according to manufacturer protocol and RNA integrity was confirmed using a TapeStation (Agilent). 210 ng of RNA from each sample was diluted in 10 uL of water as input RNA for library generation using the TruSeq Stranded Total RNA sequencing kit with RiboZero rRNA depletion (Illumina). Manufacturer instructions were followed except for substitution of SuperScriptIII for SuperScriptII. The final libraries were amplified to 10–12 cycles and purified using AMPure XP beads (Beckman Coulter). Pooled libraries (10 nM) were sequenced (paired-end 150 cycles) on an Illumina HiSeq 4000 at Novogene.
Kaye E.G., Basavaraju K., Nelson G.M., Zomer H.D., Roy D., Joseph I.I., Rajabi-Toustani R., Qiao H., Adelman K, & Reddi P.P. (2024). RNA polymerase II pausing is essential during spermatogenesis for appropriate gene expression and completion of meiosis. Nature Communications, 15, 848.
+ Open protocol
+ Expand
2

RNA-seq of Isolated Cell Types

Check if the same lab product or an alternative is used in the 5 most similar protocols
Isolated SG, RC, and RS cells were counted, and 1 × 10^6 cells were resuspended in 1mL of Trizol and spiked with 1 uL of 1:10 diluted ERCC Spike-in Mix (Invitrogen). RNA was purified according to manufacturer protocol and RNA integrity was confirmed using a TapeStation (Agilent). 210 ng of RNA from each sample was diluted in 10uL of water as input RNA for library generation using the TruSeq Stranded Total RNA sequencing kit with RiboZero rRNA depletion (Illumina). Manufacturer instructions were followed except for substitution of SuperScriptIII for SuperScriptII. The final libraries were amplified to 10–12 cycles and purified using AMPure XP beads (Beckman Coulter). Pooled libraries (10nM) were sequenced (paired-end 150 cycles) on an Illumina HiSeq 4000 at Novogene.
Kaye E.G., Nelson G.M., Zomer H.D., Roy D., Joseph I.I., Adelman K, & Reddi P.P. (2023). RNA polymerase II pausing is essential during spermatogenesis for appropriate gene expression and completion of meiosis. bioRxiv.
+ Open protocol
+ Expand
3

Illumina RNA-seq Library Preparation

Cited 1 time
Check if the same lab product or an alternative is used in the 5 most similar protocols
RNA samples were quality tested by bioanalyzer and libraries were prepared following standard protocols and Illumina reagents, including Illumina Ribo-Zero rRNA depletion [70 (link)], by the Max Planck Genome Center, Cologne, Germany, and were sequenced with single-end 100 bp reads on the Illumina HiSeq2500.
McLoon A.L., Boeck M.E., Bruckskotten M., Keyel A.C, & Søgaard-Andersen L. (2021). Transcriptomic analysis of the Myxococcus xanthus FruA regulon, and comparative developmental transcriptomic analysis of two fruiting body forming species, Myxococcus xanthus and Myxococcus stipitatus. BMC Genomics, 22, 784.
+ Open protocol
+ Expand
4

RNA Sequencing Library Preparation

Check if the same lab product or an alternative is used in the 5 most similar protocols
RNA was prepared immediately using RNeasy purification kits (Qiagen) and quantified using Qubit 3.0 (ThermoFisher). RNA integrity was assessed using Agilent BioAnalyzer RNA Pico chip. Samples were submitted for Ribo-zero rRNA depletion (Illumina) and reassessed for RNA integrity. Samples were processed into libraries by the Ovation RNA-Seq System v2 (NuGEN) protocol. Quality control was performed on libraries using the KAPA qPCR QC assay (KAPA Biosystems). Libraries (36 total) were sequenced on an illumina HiSeq 1500 at the Marshall University Genomics Core facility, 2 × 50 bp resulting in ~16 M reads per sample. Sequencing data was deposited to the Sequence Read Archive (reference number SRP130256, BioProject number PRJNA430726).
Varney M.E., Boehm D.T., DeRoos K., Nowak E.S., Wong T.Y., Sen-Kilic E., Bradford S.D., Elkins C., Epperly M.S., Witt W.T., Barbier M, & Damron F.H. (2018). Bordetella pertussis Whole Cell Immunization, Unlike Acellular Immunization, Mimics Naïve Infection by Driving Hematopoietic Stem and Progenitor Cell Expansion in Mice. Frontiers in Immunology, 9, 2376.
+ Open protocol
+ Expand
5

RNA-seq analysis of INTS8 knockdown

Check if the same lab product or an alternative is used in the 5 most similar protocols
293T cells were treated for 48 hours with either control or INTS8 targeting siRNAs as described above. Cells were harvested and washed with PBS. Cells were counted, and 1 × 106 cells were resuspended in 1mL of Trizol and spiked with 1 μL of 1:10 diluted ERCC Spike-in Mix (Invitrogen) and RNA was purified. 1 μg of RNA from each sample was diluted in 10uL of water. The input RNA was subjected to RNA-seq library generation using the TruSeq Stranded Total RNA sequencing kit with RiboZero rRNA depletion (Illumina). The final libraries were amplified to 10 cycles and purified using AMPure XP beads (Beckman Coulter). Pooled libraries (10nM) were sequenced (PE150) on the HiSeq platform at Novogene.
Reads were filtered to require a mean quality score ≥ 20, trimmed to 100 nt, and mapped to the hg38 human genome assembly using STAR. Default parameters were used, except that multimappers were randomly assigned (outMultimapperOrder Random), spurious junctions were filtered (outFilterType BySJout), minimum overhang for non-annotated junctions was set to 8 nt (alignSJoverhangMin 8), and non-canonical alignments were removed (outFilterIntronMotifs RemoveNoncanonicalUnannotated).
The total number of RNA-seq reads aligned in the control or INTS8-dep. samples is described below:
Huang K.L., Jee D., Stein C.B., Elrod N.D., Henriques T., Mascibroda L.G., Baillat D., Russell W.K., Adelman K, & Wagner E.J. (2020). Integrator Recruits Protein Phosphatase 2A to Prevent Pause Release and Facilitate Transcription Termination. Molecular cell, 80(2), 345-358.e9.
+ Open protocol
+ Expand
6

RNA-Seq Protocol for Differential Expression

Cited 2 times
Check if the same lab product or an alternative is used in the 5 most similar protocols
Between 3 and 5 μg of total RNA were sent to Admera Health LLC (NJ, USA) for sequencing in paired-end mode, 2x 150 nucleotides, using an Illumina HiSeq 2500 sequencer. The sequencing library was prepared with the NEBNext Ultra II kit, with RiboZero rRNA depletion (NEB #E7103, Illumina #20040526). Between 60 and 90 million paired end reads were obtained from each sample and mapped to the human genome (Hg38) with STAR v2.7.5a (98 (link)) using default parameters. Mapping quality was assessed with FastQC v0.11.9 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc). Sequencing adaptors were removed with trimmomatic v0.35 (99 (link)). Low-quality reads and mitochondrial contaminants were removed, leaving on average 70 million useful reads per sample (Supplementary Material, Table S1). Differential expression analysis was performed in R with DESeq2 v1.32.0 (100 (link)) after transcript quantitation with Salmon v1.4.0 (101 (link)). We used an FDR threshold of 5% for differential expression.
de las Heras J.I., Todorow V., Krečinić-Balić L., Hintze S., Czapiewski R., Webb S., Schoser B., Meinke P, & Schirmer E.C. (2022). Metabolic, fibrotic and splicing pathways are all altered in Emery-Dreifuss muscular dystrophy spectrum patients to differing degrees. Human Molecular Genetics, 32(6), 1010-1031.
+ 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!