RNA from fresh tissue was extracted by the Tissue Lyser plus Maxwell® RSC simplyRNA Tissue Kit (AS1340 Promega, Southampton, UK) in accordance with the manufacturer. Total RNA concentration was quantified by the Qubit® 2.0 Fluorometer (Invitrogen) using Qubit™ RNA High-Sensitivity (HS) Assay Kits (ThermoFisher, Waltham, MA, USA). The RNA library was prepared using the Illumina Stranded Total RNA Prep with Ribo-Zero Plus (Illumina Inc., San Diego, CA, USA). Briefly, after ribosomal and globin RNA depletion, RNA was fragmented and denatured, and cDNA synthesized. Then, the 3′ ends were adenylated, and anchors ligated, followed by a PCR amplification step to add the index-adapter sequences. After clean-up and final amplification of the dual indexed libraries, the quality of the libraries was assessed by the 2100 Bioanalyzer with a High-Sensitivity DNA chip (Agilent), and libraries concentration was assessed with a High-Sensitivity Assay on a Qubit 4 fluorometer (ThermoFisher). Libraries were then pooled at 1.4 nM and paired-end-sequenced (2 × 150) on a NovaSeq 6000 Sequencing System instrument (Illumina Inc., San Diego, CA, USA) with the addition of 1% PhiX. Run metrics were 85.13% PF (clusters Passing Filter) and 91.02 Q30. Sequencing reads were aligned to the reference genome (GENCODE GRCh38 version 33) using STAR v.2.7.3a in two-pass basic mode preventing multimappings.
Stranded total rna prep with ribo zero plus
Manufactured by Illumina
Sourced in United States
The Stranded Total RNA Prep with Ribo-Zero Plus is a laboratory equipment product designed for the preparation of stranded total RNA samples. It enables the removal of ribosomal RNA (rRNA) from total RNA, allowing for the enrichment of non-rRNA species. The product provides a streamlined workflow for generating high-quality, stranded total RNA libraries suitable for downstream sequencing and analysis.
Automatically generated - may contain errors
Lab products found in correlation
Novaseq 6000, by Illumina (2 mentions)
2100 bioanalyzer, by Agilent Technologies (2 mentions)
Direct zol rna miniprep kit, by Zymo Research (2 mentions)
Trizol, by Thermo Fisher Scientific (2 mentions)
Qubit 4 fluorometer, by Thermo Fisher Scientific (1 mentions)
Qubit rna high sensitivity assay kit, by Thermo Fisher Scientific (1 mentions)
Qubit 2.0 fluorometer, by Thermo Fisher Scientific (1 mentions)
High sensitivity dna chip, by Agilent Technologies (1 mentions)
Nextseq platform, by Illumina (1 mentions)
Dneasy blood and tissue mini kit, by Qiagen (1 mentions)
Minion platform, by Oxford Nanopore (1 mentions)
Nextera xt dna library prep kit, by Illumina (1 mentions)
Dneasy ultraclean microbial kit, by Qiagen (1 mentions)
Rneasy plus universal mini kit, by Qiagen (1 mentions)
Nextseq 2000, by Illumina (1 mentions)
Bioanalyzer, by Agilent Technologies (1 mentions)
Mastercycler pro, by Eppendorf (1 mentions)
Agencourt rnaclean xp beads, by Beckman Coulter (1 mentions)
Nextseq 1000, by Illumina (1 mentions)
Tapestation, by Agilent Technologies (1 mentions)
11 protocols using stranded total rna prep with ribo zero plus
1
Illumina-Based RNA-Seq from Fresh Tissue
2
Illumina Stranded Total RNA Sequencing
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Extracted RNA was subject to total RNA sequencing. Libraries were prepared using the Illumina Stranded Total RNA Prep with Ribo-Zero Plus (Illumina) and 16 cycles of PCR. Paired-end 150 bp sequencing of the RNA libraries was performed on the Illumina NovaSeq 6000 platform using a single S4 lane.
3
Illumina NovaSeq 6000 RNA Sequencing
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Extracted RNA was subject to total RNA sequencing. Libraries were prepared using the Illumina Stranded Total RNA Prep with Ribo-Zero Plus (Illumina) and 16 cycles of PCR.
Paired-end 150bp sequencing of the RNA libraries was performed on the Illumina NovaSeq 6000 platform.
Paired-end 150bp sequencing of the RNA libraries was performed on the Illumina NovaSeq 6000 platform.
4
Whole Genome Sequencing of Bacterial Isolates
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Genomic DNA was extracted with the DNeasy Blood and Tissue Mini Kit (QIAGEN, Germany) or DNeasy UltraClean Microbial Kit (QIAGEN, Germany) for Illumina and Nanopore sequencing, respectively. WGS was performed at the Microbial Genomics Reference Laboratory, NSW Health Pathology. All strains were short-read sequenced on the NextSeq platform (Illumina, USA). In addition, strains CIDM-BP2, CIDM-BP3, CIDM-BH3, CIDM-BPP2 and CIDM-BPP2R were also long-read sequenced on the MinION platform (Oxford Nanopore Technologies plc, UK). Sequencing libraries for Illumina sequencing were prepared using the Nextera XT DNA Library Prep Kit (Illumina) and sequenced on a NextSeq 500 using NextSeq 500/550 v2 mid output kits (Illumina). Sequencing libraries for Nanopore sequencing were prepared using the Rapid Barcoding kit (SQK-RBK004) and sequencing on a R9 flowcell. Total RNA was extracted from liquid cultures using the RNeasy Plus Universal Mini Kit (QIAGEN, Germany), following manufacturer’s protocol. Total RNA sequencing was performed by the Australian Genomics Research Facility (AGRF) utilizing the Illumina Stranded Total RNA Prep with Ribo-Zero Plus on the NovaSeq.
5
Transcriptomic Analysis of Human Samples
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Cells were lysated with TRIzol and total RNA was purfiled using Zymo Research Direct-zol RNA mini-prep kit (R2050) following manufacturer’s manual. Libraries were generated using the Illumina Stranded Total RNA Prep with Ribo-Zero Plus (20040525). 40 base-pair single-end reads were sequenced on the Illumina NextSeq 2000. Reads were aligned to hg19 human reference genome using STAR v2.5. FeatureCounts(56 (link)) was used for counting reads to the genes. Data were normlized using Voom and differential gene expression analysis was performed using DEseq2 in R (v1.38.3) unless otherwise noted. Data was visualized using ggplot2 (3.3.6). GO enrichment analysis was done using gprofiler2 package in R (v 0.2.1). Gene set enrichment analysis (GSEA) was 500 randomly selected genes from the select data set using the clusterProfiler package in R (v4.6.2). Interpro domain analysis was done using DAVID (https://david.ncifcrf.gov/tools.jsp ).
6
Ribosomal Protein S6 RNA-seq Analysis
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
RNA‐seq was performed on WT, rps6a‐2, rps6b‐1, rps6a‐2 rps6b‐1; eS6zWT‐HA, and rps6a rps6b; eS6zΔ6S > A genotypes grown under long day conditions. Twelve days after germination, the aerial portions of the seedlings were harvested by flash freezing in liquid nitrogen in the morning. Total RNA was extracted using a commercial kit. RNA quality was measured using a Bioanalyzer (Agilent). Paired‐end cDNA libraries were constructed using the Illumina Stranded Total RNA Prep with Ribo‐Zero Plus. The libraries were sequenced on a NextSeq in paired‐end mode and with 75 base pair long reads at the Oklahoma Medical Research Foundation (Oklahoma City, USA). Raw read quality was assessed with FastQC v0.11.5. Raw reads were aligned to the TAIR10.1 genome and Araport11 annotation using STAR‐2.7.7a (Dobin et al., 2013 (link)), with default parameters except for the following: ‐alignIntronMax 1000. Mapping quality was assessed with RSeQC v4.0.0 (Wang et al., 2012 (link)). Reads were counted using subread featureCounts v2.0.1 (Liao et al., 2014 (link)) in paired‐end mode.
7
Illumina Stranded Total RNA Sequencing
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Total RNA was extracted with Trizol (Thermo Fisher) and purified using Quick-RNA Miniprep Kit (Zymo Research). RNA-sequencing libraries were performed using Illumina’s total RNA kit per manufacturer’s instructions. RNA integrity was determined using an Agilent TapeStation with eRIN values > 7.500 ng of total RNA was used as input. rRNA was depleted, cDNA (first and second strands) were synthesized, and adaptor index ligation and strand selection was performed (Illumina Stranded total RNA Prep with Ribo-Zero Plus). For multiplexing, barcodes with unique indices out of 96, were used per sample (IDT for Illumina). Libraries were amplified by PCR on a Mastercycler Pro (Eppendorf) and purified with RNAClean XP Agencourt beads (Beckman Coulter). Libraries were sequenced on a NextSeq1000 (Illumina) to generate 30 M, 75-bp paired end reads per sample.
8
RNA-seq Using Direct-zol Extraction
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Total RNA was isolated from cells using the Direct-zol RNA MiniPrep kit (Zymo Research R2053), following manufacturer’s instructions. ERCC spike-in controls (ThermoFisher 4456740) were added to 500–1000 ng of total RNA. RNA was sent to the NCI CCR-Illumina Sequencing facility for library preparation and sequencing. RNA was rRNA depleted and directional cDNA libraries were generated using either Stranded Total RNA Prep with Ribo-Zero Plus (Illumina # 20040525) or TruSeq Stranded Total RNA Ribo-Zero Gold (Illumina #RS-122-2303). 2–4 biological replicates were sequenced for all samples. Sequencing was performed at the National Cancer Institute Center for Cancer Research Frederick Sequencing Facility using the Illumina NextSeq 550 or Illumina NovaSeq SP platform to generate 150 bp paired-end reads.
9
Illumina Stranded Total RNA Sequencing
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Libraries were prepared using 50 ng of total RNA (all with RIN > 8.5) according to the manufacturer’s instructions with the Illumina® Stranded Total RNA Prep with Ribo-Zero Plus (Illumina, Inc., San Diego, CA, USA), including the depletion of cytoplasmic, mitochondrial and beta globin rRNA from 0.1–1 μg of intact total RNA samples. After rRNA depletion, libraries were prepared with 50 ng of total RNA (RIN > 8.5). Library integrity was confirmed by size analysis on a 4200 TapeStation (Agilent, Santa Clara, CA, USA) with a D1000 ScreenTape. All libraries were within an average size range of 360 to 400 bp. Library integrity and size (size range of 360 to 400 bp) was confirmed by analysis on a 4200 TapeStation (Agilent, Santa Clara, CA, USA) with D1000 ScreenTape. Library concentrations were determined using the dsDNA HS assay kit on Qubit 3.0 (Thermo Fisher Scientific, Waltham, MA, USA). Sequencing was performed with paired-end 75 cycles on a NextSeq 550 System (Illumina, Inc.) at the Instituto Tecnológico y de Energías Renovables.
10
Deep Sequencing of Viral Genomes
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Viral genomes were extracted from viral stocks using TRIzol LS, following the manufacturer’s protocol. 100 ng of total RNA was used as input for the Illumina Stranded Total RNA Prep with Ribo-Zero Plus protocol. Libraries were prepared for sequencing on a MiSeq instrument following the manufacturer’s protocol and sequenced on a 150v3 chip with at least 500,000 reads per sample. Reads were aligned to the DENV genome using STAR with the parameters --peOverlapNbasesMin 30 --outSAMtype BAM SortedByCoordinate. BAM files were imported into Geneious Prime and variants with >100 read coverage and >2% frequency were called. Coverage was greater than 20,000X. See Supplementary Fig. 1B for results. Reference codon and percent of change in codon are reported, for example at nucleotide position 1675 the reference codon was aac (aa N) was found in 94.1% of the reads and the changed codon cac (aa H) was found in 5.9% of the reads.
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
Revolutionizing how scientists
search and build protocols!