Agilent 4200 system

Manufactured by Agilent Technologies

Sourced in United States, Germany

The Agilent 4200 system is a compact and versatile laboratory instrument designed for analytical applications. It features a modular and configurable design, allowing for adaptability to various testing requirements. The system provides fundamental functionality for analytical tasks, without further interpretation or extrapolation on its intended use.

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Lab products found in correlation

Nanodrop one, by Thermo Fisher Scientific (4 mentions) Qubit dsdna hs assay kit, by Thermo Fisher Scientific (2 mentions) Novaseq 6000, by Illumina (2 mentions) S1000 touch thermal cycler, by Bio-Rad (2 mentions) Chromium single cell controller, by 10x Genomics (2 mentions) Novaseq 6000 sequencer, by Illumina (2 mentions) Repli g cell wga wta kit, by Qiagen (1 mentions) Minibest viral rna dna extraction kit, by Takara Bio (1 mentions) Nebnext ultra dna library prep kit, by New England Biolabs (1 mentions) Ribo zero gold kit, by Illumina (1 mentions) Qubit 3.0 fluorometer, by Thermo Fisher Scientific (1 mentions) Novaseq 6000 platform, by Illumina (1 mentions) Mrna seq prep kit, by Illumina (1 mentions) Qubit 2.0 fluorometer, by Thermo Fisher Scientific (1 mentions) Hiseq 2000 sequencing platform, by Illumina (1 mentions) Nanodrop 1000 spectrophotometer, by Thermo Fisher Scientific (1 mentions) Qubit 3, by Thermo Fisher Scientific (1 mentions) Qubit r dsdna hs assay kit, by Thermo Fisher Scientific (1 mentions) Chromium single cell g chip kit, by 10x Genomics (1 mentions) Single cell 3 library and gel bead kit v3, by 10x Genomics (1 mentions)

Spelling variants of this product

Agilent 4200 TapeStation System (188 citations) Agilent 4200 (51 citations) Agilent 2100/4200 system (6 citations)

10 protocols using agilent 4200 system

Viral Genome Sequencing and Analysis

Cited 3 times

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Virus DNA was extracted using MiniBEST Viral RNA/DNA Extraction Kit (TaKaRa, Dalian, China), and the whole genome was amplified with REPLI-g Cell WGA & WTA Kit (Qiagen, Hilden, Germany).
Sequencing libraries were generated using NEB Next^® Ultra™ DNA Library Prep Kit (New England Biolabs, MA, United States) following the manufacturer’s recommendations and index codes were added. The library quality was assessed using the Qubit^® dsDNA HS Assay Kit (Life Technologies, Grand Island, NY) and Agilent 4200 system (Agilent, Santa Clara, CA). The libraries were sequenced on an Illumina NovaSeq 6000 and 150 bp paired-end reads were generated. The raw data in this study have been deposited in the GenBank Sequence Read Archive database. The accession number is PRJNA797730.
The raw data processing with SOAPnuke (v1.5.6; Chen et al., 2018 (link)) were conducted to acquire the clean data for subsequent analysis. To remove the host sequence, clean reads were compared with the ribosome database (Silva.132) and host reference genome of Pacific white shrimp (NCBI Project ID: PRJNA438564; Zhang et al., 2019 (link)), respectively, with Burrows-Wheeler Aligner (BWA) software (v0.7.17, parameter: mem –k 30; Li and Durbin, 2009 (link)). The results that comparison length was less than 80% of the length of reads would be filtered, and then removed the host sequence (Li and Durbin, 2009 (link)).

Deng Z., Zeng S., Zhou R., Hou D., Bao S., Zhang L., Hou Q., Li X., Weng S., He J, & Huang Z. (2022). Phage-prokaryote coexistence strategy mediates microbial community diversity in the intestine and sediment microhabitats of shrimp culture pond ecosystem. Frontiers in Microbiology, 13, 1011342.

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Transcriptomic Analysis of Gingival Tissues

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Total RNA was isolated from gingival tissues by using a TaKaRa MiniBEST Universal RNA Extraction Kit according to the manufacturer's instructions. The RNA quality was determined using a Qubit^®3.0 Fluorometer (Life Technologies). RNA integrity was measured using an Agilent 4200 system (Agilent Technologies).
A total of 1 μg of RNA per sample was used as the initial material for RNA sample preparation. Ribosomal RNA was removed using Ribo‐Zero™ Gold Kits (Epicentre). Subsequently, the sequencing libraries were generated following the manufacturer's recommendations with different index labels by using the NEBNext^® Ultra™ Directional RNA Library Prep Kit for Illumina (NEB). The libraries were clustered and sequenced on the Illumina NovaSeq 6000 platform, and 150 bp paired‐end reads were generated. Raw reads (fastq files) were aligned to the reference genome GRCh38 using the High‐performance Integrated Virtual Environment (HIVE).

Jiang Y., Fang B., Xu B, & Chen L. (2019). The RAS‐PI3K‐AKT‐NF‐κB pathway transcriptionally regulates the expression of BCL2 family and IAP family genes and inhibits apoptosis in fibrous epulis. Journal of Clinical Laboratory Analysis, 34(3), e23102.

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RNA Extraction and RNA-Seq Library Preparation

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The RNA was extracted using a sample RNA extraction kit by TIANGEN (Beijing, China). In order to ensure the quality of the samples used for transcriptome sequencing, the purity, concentration, and integrity of the RNA samples were determined using a Nanodrop 1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA), a Qubit 2.0 fluorometer (Invitrogen, Waltham, MA, USA), and an Agilent 4200 system (Agilent Technologies, Santa Clara, CA, USA). An Illumina mRNA-Seq Prep Kit was used for preparing the RNA samples for the RNA-seq libraries, which were subsequently sequenced by paired-end sequencing on an Illumina HiSeq 2000 sequencing platform (Illumina, San Diego, CA, USA).

Wang Y., Chen R., Wang Q., Yue Y., Gao Q., Wang C., Zheng H, & Peng S. (2022). Transcriptomic Analysis of Large Yellow Croaker (Larimichthys crocea) during Early Development under Hypoxia and Acidification Stress. Veterinary Sciences, 9(11), 632.

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Transcriptional Response of L. acidophilus During Salmonella Infection

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On day 14 post-infection, three mice per group were euthanized, and 2 cm-long small intestine tissue samples (ileum) were collected to analyze the transcriptional response of L. acidophilus during Salmonella infection. Total RNA was isolated using the TRIzol method [109 (link)], following the manufacturer’s instructions (Magigene Biotechnology Co., Ltd., Guangzhou, China). The integrity of the RNA was assessed using the Agilent 4200 system (Agilent Technologies, Waldbronn, Germany), and the RNA concentration was determined using NanoDrop One (Thermo Fisher Scientific, Waltham, MA, USA).

Junaid M., Lu H., Din A.U., Yu B., Liu Y., Li Y., Liu K., Yan J, & Qi Z. (2024). Deciphering Microbiome, Transcriptome, and Metabolic Interactions in the Presence of Probiotic Lactobacillus acidophilus against Salmonella Typhimurium in a Murine Model. Antibiotics, 13(4), 352.

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RNA Extraction and Sequencing of L. paraplantarum RX-8

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Cell samples of L. paraplantarum RX-8 were obtained in co-culture and mono-culture at 24 h by centrifugation (10,000 rpm, 10 min, 4°C). After removing the supernatant, cells were immediately cleaned by phosphate buffered saline (PBS) two times, frozen in liquid nitrogen for 15 min, and then stored at −80°C.
Total RNA extractions were performed using Magen HiPure Universal RNA Kit (Magen, China). RNA concentration and purity were measured using Qubit 3.0 (Thermo Fisher Scientific, MA, USA) and Nanodrop One (Thermo Fisher Scientific, MA, USA), and integrity was confirmed using the Agilent 4200 system (Agilent Technologies, Waldbron, Germany). The RNA samples with an RNA integrity number (RIN) >6.5, and 280/260 ratios >1.5 were further used for RNA-sequencing purposes. Libraries were generated from three replicates using NEB Next^®Ultra™ Directional RNA Library Prep Kit for Illumina^® (New England Biolabs, MA, USA). From these libraries, the PE150 reads were produced with the Illumina Novaseq6000 platform by Guangdong Magigene Biotechnology Co., Ltd. (Guangzhou, China). All raw RNA-Seq data were submitted to NCBI under BioProject PRJNA901346.

Nie R., Zhu Z., Qi Y., Wang Z., Sun H, & Liu G. (2023). Bacteriocin production enhancing mechanism of Lactiplantibacillus paraplantarum RX-8 response to Wickerhamomyces anomalus Y-5 by transcriptomic and proteomic analyses. Frontiers in Microbiology, 14, 1111516.

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Illumina Sequencing Library Preparation

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Sequencing libraries were generated using the NEB Next^® Ultra™ DNA Library Prep Kit for Illumina^® (NewEngland Biolabs, Ipswich, MA, USA) following the manufacturer’s recommendations. The main steps include: (1) DNA sequence amplification and product fragmentation; (2) end repair and 3′ end plus A; (3) adaptor ligation, fragment selection, and purification; and (4) PCR amplification and purification. The library quality was assessed using the Qubit R dsDNA HS Assay Kit (Life Technologies, Grand Island, NY, USA) and Agilent 4200 system (Agilent, Santa Clara, CA, USA). High-throughput sequencing was conducted on an Illumina Novaseq 6000 and 150 bp paired-end reads were generated by the Magigene Company (Guangzhou, China).

Gao J., Liu C., Yi J., Shi Y., Li H, & Liu H. (2023). Genomic Characteristics of Feline Anelloviruses Isolated from Domestic Cats in Shanghai, China. Veterinary Sciences, 10(7), 444.

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Single-cell RNA-seq using 10x Genomics

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Using the single‐cell 3′ Library and Gel Bead Kit V3.1 (10x Genomics, 1000121) and the Chromium Single Cell G Chip Kit (10x Genomics, 1000120), the cell suspension was loaded onto the Chromium Single Cell Controller (10x Genomics) to generate single‐cell gel beads in the emulsion according to the manufacturer's protocol. In short, single cells were suspended in phosphate‐buffered saline containing 0.04% bovine serum albumin. About 6000 cells were added to each channel, and the target number of cells to be recovered was estimated to be about 3000 cells. Captured cells were lysed, and the released RNA was barcoded through reverse transcription in individual GEMs. Reverse transcription was performed on an S1000TM Touch Thermal Cycler (Bio Rad) at 53°C for 45 min, followed by 85°C for 5 min, and then held at 4°C. The cDNA was generated and then amplified, and quality was assessed using an Agilent 4200 system (performed by CapitalBio Technology, Beijing, China). According to the manufacture's introduction, scRNA‐seq libraries were constructed using the Single Cell 3′ Library and Gel Bead Kit V3.1. Finally, the libraries were sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100,000 reads per cell with the paired‐end 150 bp strategy (performed by CapitalBio Technology, Beijing, China).

Li Y., Li X., Chen H., Sun K., Li H., Zhou Y., Wang J., Bai F, & Yang F. (2022). Single‐cell RNA sequencing reveals the multi‐cellular ecosystem in different radiological components of pulmonary part‐solid nodules. Clinical and Translational Medicine, 12(2), e723.

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Single-cell RNA Sequencing Using 10x Genomics

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Cell capture and cDNA synthesis were carried out using a single-cell 5′ Library and Gel Bead Kit (10x Genomics, 1000006) and a Chromium Single Cell A ChIP Kit (10x Genomics, 120236). The cell suspension (300-600 viable cells per microliter, as measured with a Countstar system) was loaded onto the Chromium single-cell controller (10x Genomics) to generate single-cell gel beads in emulsion according to the manufacturer’s protocol. In brief, single cells were suspended in PBS containing 0.04% BSA. Captured cells were lysed, and the released RNA was barcoded through reverse transcription in individual gel beads in emulsion (GEMs). Reverse transcription was performed on an S1000TM Touch Thermal Cycler (Bio-Rad) with the following thermal cycling program: 53 °C for 45 min, followed by 85 °C for 5 min and holding at 4 °C. cDNA was generated and then amplified, and the quality was assessed using an Agilent 4200 system (performed by CapitalBio Technology, Beijing).

Luo F., Li H., Ma W., Cao J., Chen Q., Lu F., Qiu M., Zhou P., Xia Z., Zeng K., Zhan J., Zhou T., Luo Q., Pan W., Zhang L., Lin C., Huang Y., Zhang L., Yang D, & Zhao H. (2023). The BCL-2 inhibitor APG-2575 resets tumor-associated macrophages toward the M1 phenotype, promoting a favorable response to anti-PD-1 therapy via NLRP3 activation. Cellular and Molecular Immunology, 21(1), 60-79.

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Illumina Library Preparation and Sequencing

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Following manufacturer's instructions, the Next® Ultra™DNA Library Prep Kit for Illumina® (New England Biolabs) was used to generate the sequencing libraries and add the index codes. The library quality was assessed by the Qubit® dsDNA HS Assay Kit (Life Technologies) and Agilent 4,200 system (Agilent, Santa Clara). High-throughput sequencing was conducted on an Illumina Novaseq 6,000 and 150 bp paired-end reads were generated by the Magigene Company (Guangzhou, China). Eighteen libraries were then constructed (Supplementary Table 1).

Shi Y., Tao J., Li B., Shen X., Cheng J, & Liu H. (2021). The Gut Viral Metagenome Analysis of Domestic Dogs Captures Snapshot of Viral Diversity and Potential Risk of Coronavirus. Frontiers in Veterinary Science, 8, 695088.

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Single-cell RNA-seq Library Prep

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Using a Single Cell 5′ Library & Gel Bead Kit (10× Genomics) and Chromium Single Cell A Chip Kit (10× Genomics), cell suspensions (300–600 living cells/µL as determined by Countstar) were loaded onto a Chromium Single-cell controller (10× Genomics) to generate single-cell gel beads in emulsion (GEMs) according to the manufacturer’s protocol. Briefly, single cells were suspended in phosphate-buffered saline (PBS) containing 0.04% bovine serum albumin (BSA). The cells were added to each channel, and approximately 50% of input cells were recovered. The captured cells were lysed, and the released RNA was barcoded through reverse transcription in individual GEMs. Reverse transcription was performed on a S1000™ Thermal Cycler (Bio-Rad Laboratories, Hercules, CA) at 53 °C for 45 min, followed by 85 °C for 5 min, and held at 4 °C. Complementary DNA (cDNA) was generated and amplified, and its quality was assessed using an Agilent 4200 system (performed by CapitalBio Technology, Beijing, China). Following the manufacturer’s introductions, scRNA-seq libraries were constructed using a Single Cell 5′ Library & Gel Bead Kit, Single Cell V(D)J Enrichment Kit, and Human T Cell (1000005). The libraries were sequenced using an Illumina NovaSeq 6000 sequencer with a paired-end 150 bp (PE150) reading strategy (performed by CapitalBio Technology, Beijing, China).

Wang X.M., Zhang J.Y., Xing X., Huang H.H., Xia P., Dai X.P., Hu W., Zhang C., Song J.W., Fan X., Wu F.Y., Liu F.H., Ke Y., Zhao Y., Jiang T.J., Wang L.F., Jiao Y.M., Xu R.N., Jin L., Shi M., Bai F, & Wang F.S. (2022). Global transcriptomic characterization of T cells in individuals with chronic HIV-1 infection. Cell Discovery, 8, 29.

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