Total RNA was extracted from ~200 ml of Mab cells containing either vapC5-pMC1s or empty pMC1s grown for 6 hrs with the addition of 200 ng/mL ATc. Cells were centrifuged at 2300 × g at 4 °C for 10 min, cell pellets resuspended in 1 ml of Tri reagent (Zymo Research) and transferred to 2 ml lysing kits tubes (Bertin Corp.) containing 0.1 mm glass beads. Cells were lysed with a Precellys Evolution homogenizer (Bertin Corp.) using four 30 s cycles with the agitation set to 9000 rpm interspersed with 2 min cooling periods. The lysate was centrifuged at 16,000 × g for 5 min at 4 °C and RNA was isolated from the supernatant using the Direct-zol RNA Miniprep Plus extraction kit (Zymo Research). Isolated RNA was subsequently treated with 1 U of Turbo DNase for 30 min at 37 °C and purified and eluted in 45 μl of RNase-free water using the RNA Clean and Concentrator kit (Zymo Research). The RNA concentration was measured using a BioSpectrometer (Eppendorf) with a μCuvette.
Direct zol rna miniprep plus extraction kit
Manufactured by Zymo Research
Sourced in United States
The Direct-zol RNA Miniprep Plus extraction kit is a laboratory equipment product that facilitates the isolation and purification of total RNA from various sample types, including cells, tissues, and biofluids. It utilizes a rapid, single-step extraction method to obtain high-quality RNA suitable for downstream applications such as RT-qPCR, RNA-seq, and microarray analysis.
Automatically generated - may contain errors
Lab products found in correlation
Rna clean and concentrator kit, by Zymo Research (2 mentions)
Biospectrometer, by Eppendorf (2 mentions)
Tri reagent, by Zymo Research (2 mentions)
Steponeplus real time pcr system, by Thermo Fisher Scientific (1 mentions)
Revertaid first strand cdna synthesis kit, by Thermo Fisher Scientific (1 mentions)
Rt2 first strand kit, by Thermo Fisher Scientific (1 mentions)
Qubit 3 fluorometer, by Thermo Fisher Scientific (1 mentions)
Agilent 4200 tapestation system, by Agilent Technologies (1 mentions)
4 protocols using direct zol rna miniprep plus extraction kit
1
Total RNA Extraction from Mab Cells
2
Quantitative PCR Analysis of 3D Retinal Organoids
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
RNA was extracted from 3D retinal organoids using a Direct-zol™ RNA MiniPrep Plus extraction kit (Zymo Research). RNA quantity and quality were assessed using a Nanodrop system (Themo Fisher Scientific). Following this, cDNA was amplified using the RT2 First Strand Kit (RevertAid First Strand cDNA Synthesis Kit, Thermo Fisher Scientific) following the manufacturer’s instructions. qPCR was performed with TaqMan Fast Advance Mastermix and primer pairs listed in Supplementary Table 1 and analysed using a StepOnePlus™ Real-Time PCR System (AppliedBio systems™). Gene expression was normalised to glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and expressed as relative expression over 3D aggregates (spheroids) on day 0 of differentiation (self-aggregated spheroids) in AMM culture experiments, and over undifferentiated hPSCs (~ 80% confluent culture) in 2D/3D culture experiments, using a cut-off Ct value of 40. qPCR was performed in triplicate and data analysis using GAPDH and Ct values was performed as previously described39 (link) using GraphPad Prism software (version 8.0). Differentiation experiments for each protocol were analysed as separate data sets.
3
M. smegmatis Total RNA Extraction
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
In order to extract total RNA, ~50 ml of M. smegmatis cells were collected by centrifugation at 2000 g at 4°C for 5 min. Cell pellets were resuspended in Tri reagent (Zymo Research) and transferred to 2 ml lysing kit tubes (Bertin Corp.) containing 0.1 mm glass beads. Cells lysis was performed on a Precellys Evolution homogenizer (Bertin Corp.) by three consecutive 30-s pulses at 9,000 rpm, with 1 min cooling periods on ice in between each cycle. The samples were centrifuged for 5 min at 14,000 rpm at 4°C, and RNA was isolated from the supernatant using the Direct-zol RNA Miniprep Plus extraction kit (Zymo Research). After isolation, the samples were treated with 1 U of Turbo DNase as an extra genomic DNA removal step, purified using the RNA Clean and Concentrator kit (Zymo Research) and eluted in 40 μl of RNase-free water. RNA concentration was measured in a BioSpectrometer (Eppendorf) with a µCuvette.
4
Sequencing SARS-CoV-2 Genomes from Swabs
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Nucleic acid samples were extracted directly from oro-pharyngeal swab samples using a Direct-zol™ RNA MiniPrep Plus extraction kit (Zymo Research, Irvine, CA, U.S.A.) and in full compliance to the manufacturers’ recommendations. Reverse transcription and multiplex PCR were performed on the basis of information provided by the Artic Network initiative [6 (link)]. Both the concentration and the quality of the PCR products were measured and checked using the Agilent 4200 TapeStation System (Agilent Technologies, Santa Clara, CA, U.S.A.) and ThermoFisher Scientific Qubit 3 Fluorometer (Thermo Fisher Scientific, Waltham, MA, United States). The 32 sequencing libraries were prepared using 98 overlapping amplicons covering the whole viral genome. The libraries were then quantitatively checked, barcoded, and sequenced on 5 flow cells using Oxford Nanopore MinION Flow Cells (R9.4.1) (Oxford Nanopore Technologies, Littlemore, Oxford OX4 4DQ, United Kingdom).
During primary data analysis, we used RAMPART to track the sequencing process in “real-time” in order to acquire instant information regarding the quality of samples and the coverage of the amplicons. Sequencing reads of samples with sufficient amplicon coverage were mapped and consensus sequences generated by the bioinformatics pipeline built within the Artic Network protocol.
During primary data analysis, we used RAMPART to track the sequencing process in “real-time” in order to acquire instant information regarding the quality of samples and the coverage of the amplicons. Sequencing reads of samples with sufficient amplicon coverage were mapped and consensus sequences generated by the bioinformatics pipeline built within the Artic Network protocol.
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!