DNA was extracted from collected fecal samples using the EZNA tool DNA extraction kit (Omega, D4015), and the V3-V4 variable region was amplified with 16s rRNA primers. According to Gene Tools Analysis Software mixed PCR products inequal ratios, purification of PCR products, and sequencing libraries were generated using NEBNEXT Ultra DNA. Library quality was assessed using the Qu bit 2.0 Fluorometer and the Agilent Bioanalyzer 2100 system, then the library was sequenced on an Illumina Hiseq platform, 280 bp paired-end reads were generated following the sequencing libraries to analyze intestinal gut microbiota composition.
Bioanalyzer 2100 system
Manufactured by Illumina
Sourced in China, United States
The Bioanalyzer 2100 system is an automated electrophoresis platform that provides automated analysis of DNA, RNA, proteins, and cells. It utilizes microfluidic technology to perform highly sensitive and quantitative analysis of samples.
Automatically generated - may contain errors
Lab products found in correlation
Hiseq 2500 platform, by Illumina (9 mentions)
Trizol reagent, by Thermo Fisher Scientific (6 mentions)
Novaseq platform, by Illumina (4 mentions)
Hiseq 2500, by Illumina (3 mentions)
Trizol, by Thermo Fisher Scientific (3 mentions)
Ampure xp system, by Beckman Coulter (3 mentions)
Ribo zero rrna removal kit, by Illumina (3 mentions)
Hiseq 2000 platform, by Illumina (3 mentions)
Qubit 2.0 fluorometer, by Thermo Fisher Scientific (3 mentions)
Hiseq platform, by Illumina (2 mentions)
Qubit rna assay kit, by Thermo Fisher Scientific (2 mentions)
Nanophotometer spectrophotometer, by Implen (2 mentions)
Hiseq 2000, by Illumina (2 mentions)
Novaseq 6000 platform, by Illumina (2 mentions)
Rna nano 6000 assay kit, by Agilent Technologies (2 mentions)
Nanodrop 2000, by Thermo Fisher Scientific (2 mentions)
Hiseq 4000, by Illumina (2 mentions)
Human ht 12 v4 array, by Illumina (2 mentions)
Rneasy plus mini kit, by Qiagen (2 mentions)
Qubit 2.0 fluorometer, by Agilent Technologies (1 mentions)
41 protocols using bioanalyzer 2100 system
1
Gut Microbiome Analysis via 16S rRNA Sequencing
2
Directional RNA-Seq Library Preparation from Ocular Tissues
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
An Epicenter Ribo-Zero rRNA Removal Kit (Epicenter, Charlotte, NC) was used to remove the rRNA from the total RNA extracted from the right eye posterior poles of the normal control, FDM, and LIM groups (n = 3/group). The rRNA-depleted RNA was precipitated with ethanol and used to generate sequencing libraries with a NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs, Ipswich, MA) following the manufacturer’s procedures. Finally, the library quality was assessed on an Agilent Bioanalyzer 2100 system, and the libraries were sequenced on a HiSeq 4000 platform (Illumina, San Diego, CA).
3
Small RNA Sequencing Library Prep
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
In total, 3 μg total RNA per sample was used as input material for the small RNA library. NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB, United States) was used to generate the sequencing libraries following the manufacturer’s instructions. Last, PCR products corresponding to 140-160 bp (the length of small non-coding RNA plus the 3′ and 5′ adapters) were purified and recovered. Library quality was assessed using the Agilent Bioanalyzer 2100 system and then sequenced on an Illumina Hiseq 2500 platform (Novogene Biotech, China). As a result, 50-bp single-end and no less than 10 million reads were generated for each sample.
4
RNA-Seq Analysis of Verbena Roots
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Roots with two different treatments were collected from V. bonariensis. RNA-Seq analysis were performed with three replicates. Total RNA isolation was performed with Trizol Reagent (Invitrogen) according to the manufacturer’s protocol. RNA purity and concentration were checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA) and Qubit® RNA Assay Kit in Qubit® 2.0 Flurometer (Life Technologies, CA, USA), respectively. In brief, mRNA was enriched from total RNA using poly-T-oligo-attached magnetic beads. as template to synthesize double stranded cDNA, mRNAs were purified with AMPure XP beads (Beckman Coulter, Beverly, USA). the purified double stranded cDNA was subjected to terminal repair and then supplemented with A tail to connect sequencing connector. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system. At last, PCR was performed with Phusion High-Fidelity DNA polymerase, universal PCR primers and Index (X) Primer. The qualifed libraries assessed on the Agilent Bioanalyzer 2100 system were sequenced on an Illumina Hiseq2500 platform.
5
Transcriptome Analysis of Spodoptera litura Midgut
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
A total of 180 fifth-instar larvae were divided into three groups (60 larvae in each group) and treated with 3% coumarin. The high quality of RNA from S. litura midgut in each group was used for cDNA library construction based on Illumina’s protocols, and cDNA libraries were constructed with the TruSeq RNA Sample Preparation Kit v2 (Illumina, San Diego, CA, USA). Then, the prepared libraries were evaluated on an Agilent BioAnalyzer 2100 system, followed by sequencing on an Illumina HiSeq platform at Novogene (Tianjin, China). The obtained raw reads in fastq format were further processed to remove contained N base and low quality of reads using in-house perl scripts. The Q30 (percentage of sequences with sequencing error rate lower than 0.1%), Q20 (percentage of sequences with sequencing error rate lower than 1%), and the GC content of the clean data were determined.
6
Sequencing of lncRNA and miRNA Libraries
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Total RNA from each sample was used to construct lncRNA and miRNA library using the TruSeq Small RNA Sample Preparation Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instruction.
For lncRNA libraries construction, the ribosomal RNA was removed by Epicentre Ribo-zero™ rRNA Removal Kit (Epicentre, USA), and rRNA free residue was cleaned up via ethanol precipitation. Sequencing libraries were then generated using the rRNA-depleted RNA by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations. The library quality was assessed on the Agilent Bioanalyzer 2100 system and sequenced on an Illumina Hiseq 2500 platform.
For miRNA libraries construction, we used the NEB Next Multiplex Small RNA Library Prep Kit (NEB, USA) following the manufacturer’s protocol. In brief, the RNA 3′ adaptor was specifically ligated to miRNA with the excess adaptor removed by hybridization. The 5′ ends of miRNA were then ligated to the 5′ adaptor, followed by reverse transcription to convert the ligated small RNA into cDNA, which was then uniquely indexed by PCR to generate the sequencing library. The quantified libraries were clustered to a flow cell and sequenced using TruSeq SBS Kit on a HiSeq system (Illumina).
For lncRNA libraries construction, the ribosomal RNA was removed by Epicentre Ribo-zero™ rRNA Removal Kit (Epicentre, USA), and rRNA free residue was cleaned up via ethanol precipitation. Sequencing libraries were then generated using the rRNA-depleted RNA by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations. The library quality was assessed on the Agilent Bioanalyzer 2100 system and sequenced on an Illumina Hiseq 2500 platform.
For miRNA libraries construction, we used the NEB Next Multiplex Small RNA Library Prep Kit (NEB, USA) following the manufacturer’s protocol. In brief, the RNA 3′ adaptor was specifically ligated to miRNA with the excess adaptor removed by hybridization. The 5′ ends of miRNA were then ligated to the 5′ adaptor, followed by reverse transcription to convert the ligated small RNA into cDNA, which was then uniquely indexed by PCR to generate the sequencing library. The quantified libraries were clustered to a flow cell and sequenced using TruSeq SBS Kit on a HiSeq system (Illumina).
7
Extracting and Sequencing Plant Transcriptome
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Total RNA from foliage samples of MM, MM- R3a-Avr3a, and MM-Avr3a plants after spraying DEX, with three bio-replicates, were extracted as described in the literature (Yang et al., 2020 (link)). High integrity RNA was use to construct the sequencing library. Libraries were generated using NEB Next® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA). The library quality was assessed using the Agilent Bioanalyzer 2100 system and RNA-sequencing was performed using the Illumina Hiseq2500 platform hosted by Biomarker Technologies CO., LTD (BTC, Beijing, China; http://www.biomarker.com.cn/ ); and 150-bp paired-end reads were generated.
8
RNA Extraction, Library Prep, and RNA-seq
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Total RNA was isolated using the TRIzol reagent (Invitrogen; #15596026), treated with DNase I, and purified using RNeasy Mini columns (Qiagen; #74034). The purity and quantity of the total RNA was measured using a Nanodrop 2000 (Thermo Scientific). The integrity of the RNA was assessed using a Bioanalyzer 2000 system (Agilent Technologies).
The library was constructed according to Novogene’s (Beijing, China) procedure, as previously described (13 (link)). Briefly, 3 μg of total RNA were utilized for the RNA sample preparations. rRNA was removed using the Ribo-zero™ rRNA removal kit (Epicentre) and the residual RNAs were cleaned up by ethanol precipitation. Subsequently, sequencing libraries were generated based on the rRNA-depleted RNA by using NEBNext® Ultra™ directional RNA library prep kit from Illumina® (Lincoln, NE) following the manufacturer’s recommendations. After library quality was assessed on an Agilent Bioanalyzer 2100 system, RNA-seq was performed on the Illumina Hiseq 2500 platform by Novogene.
The library was constructed according to Novogene’s (Beijing, China) procedure, as previously described (13 (link)). Briefly, 3 μg of total RNA were utilized for the RNA sample preparations. rRNA was removed using the Ribo-zero™ rRNA removal kit (Epicentre) and the residual RNAs were cleaned up by ethanol precipitation. Subsequently, sequencing libraries were generated based on the rRNA-depleted RNA by using NEBNext® Ultra™ directional RNA library prep kit from Illumina® (Lincoln, NE) following the manufacturer’s recommendations. After library quality was assessed on an Agilent Bioanalyzer 2100 system, RNA-seq was performed on the Illumina Hiseq 2500 platform by Novogene.
9
Total RNA Extraction and mRNA Purification for RNA-Seq
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Total RNA was extracted from collected samples using TRIzol (Invitrogen) according to the manufacturer’s protocol. Briefly, brain tissues of largemouth bass (50 mg) were homogenized in TRIzol reagent, and then chloroform and isopropanol were added to the tissue homogenate to separate the total RNA. Subsequently, mRNA was purified from the total RNA using poly-T oligo-attached magnetic beads, fragmented using divalent cations under elevated temperature and prepared for cDNA synthesis. The first and second strands cDNA were synthesized using a random hexamer primer, M-MuLV Reverse Transcriptase, and DNA Polymerase I with RNase H, respectively. After end repair and adaptor ligation, cDNA fragments of 370-420 bp in length were selected using the AMPure XP system (Beckman Coulter, Beverly, USA). PCR was then performed with Phusion High-Fidelity DNA polymerase, and the PCR products were purified for library construction. The library quality was assessed using the Agilent Bioanalyzer 2100 system and sequenced on an Illumina Novaseq platform (27 (link)).
10
Exosomal Small RNA Sequencing
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
In total, 5 ng RNA from exosomes per sample was used for small RNA library preparation. Sequencing libraries were generated using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA). The library quality was assessed on an Agilent Bioanalyzer 2100 system using DNA High Sensitivity Chips and sequenced on an Illumina HiSeq 2500/2000 platform. Known miRNAs were identified by comparison with the sequences in the miRBase 20.0 database (https://mirbase.org/ )82 (link). Differential expression analysis (exosomes from chow-diet group vs. exosomes from HFFC-diet group) was performed using the DEGseq (2010) package in R. Small RNA sequencing and analysis were performed by NovogeneCo., Ltd. (Beijing, China).
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!