Control group, SCOP group, and CK2 group of mice were sacrificed, and brains were isolated as described earlier. And total RNA was purified using Trizol as per manufacturer’s protocol. Evaluate RNA integrity was using the Agilent 2,100 Bioanalyzer with an RNA LabChip Kit (Agilent Technologies). cDNA was prepared from total RNA using a random priming method followed by fragmentation of double-stranded cDNA, labelling and hybridization onto the GeneChip WT Terminal Labeling and Controls Kit. Microarrays were scanned with the Affymetrix GeneChip Scanner 3,000 7G. Raw data using Affymetrix GeneChip Operating Software. The obtained data were screened, and the differentially expressed genes were analyzed by unsupervised hierarchical clustering and displayed as heatmap. The GO Enrichment Analysis method uses the differential gene to perform gene function annotation based on the GO database (http://www.geneontology.org ). Obtain the molecular function of the gene, and then screen out the significant function of the gene. Calculate the significance level (p-value) and false positive rate (FDR) of each function using Fisher’s exact test and multiple comparison test. The standard of significant screening: p-value < 0.01.
Rna labchip kit
Manufactured by Agilent Technologies
Sourced in United States
The RNA LabChip Kit is a laboratory instrument designed for the analysis and quantification of RNA samples. It provides a standardized and automated approach to assess the quality and integrity of RNA samples, which is a critical step in various molecular biology workflows.
Automatically generated - may contain errors
Lab products found in correlation
Agilent 2100 bioanalyzer, by Agilent Technologies (7 mentions)
Trizol reagent, by Thermo Fisher Scientific (5 mentions)
Nanodrop nd 1000 spectrophotometer, by Thermo Fisher Scientific (3 mentions)
Nanodrop 1000 spectrophotometer, by Thermo Fisher Scientific (2 mentions)
Rneasy mini kit, by Qiagen (2 mentions)
2100 bioanalyzer, by Agilent Technologies (2 mentions)
Nanodrop 1000, by Thermo Fisher Scientific (2 mentions)
Genechip scanner 3000 7g, by Thermo Fisher Scientific (1 mentions)
Rt2 first strand kit, by Qiagen (1 mentions)
Aurum total rna mini kit, by Bio-Rad (1 mentions)
Revertaid first strand synthesis kit, by Thermo Fisher Scientific (1 mentions)
7500 real time pcr system, by Thermo Fisher Scientific (1 mentions)
Taqman gene expression assay, by Thermo Fisher Scientific (1 mentions)
Genejet rna purification kit, by Thermo Fisher Scientific (1 mentions)
Genechip ht ivt labeling kit, by Thermo Fisher Scientific (1 mentions)
Genechip 3 ivt express kit, by Thermo Fisher Scientific (1 mentions)
Agilent rna 6000 nano kit, by Agilent Technologies (1 mentions)
Tri reagent, by Merck Group (1 mentions)
Agilent bioanalyzer, by Agilent Technologies (1 mentions)
Rna seq, by Illumina (1 mentions)
14 protocols using rna labchip kit
1
Transcriptomic Analysis of Mouse Brain
2
Comprehensive RNA Isolation and Analysis Protocol
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Total RNA was isolated using Aurum Total RNA Mini Kit (Bio-Rad, cat #732-6820). RNA quality was verified using RNA LabChip Kit (Agilent, RNA 6000 Nano) and concentration measured with a NanoDrop ND-1000 spectrophotometer (Thermo Scientific). One microgram of total RNA was converted to cDNA using RevertAid First Strand Synthesis Kit (Thermo Scientific, K1621) and RT2 First Strand Kit (SABiosciences, cat #330401). The level of specific transcripts was assessed using RT2 Profiler PCR Array Human Fibrosis (SABiosciences, cat #PAHS-120) according to the manufacturer's protocols. Confirmation of RT2 Profiler PCR Array was performed by Q-PCR analysis using TaqMan Gene Expression Assays (Applied Biosystems, cat #4331182). All PCR reactions were performed using 7500 Real-Time PCR System (Applied Biosystems). RT2 Profiler PCR Array data were analyzed using RT2 Profiler Array Data Analysis Version 3.5 Software. RT-
RCR data were analyzed using comparative ΔΔCt method. If not specified, GAPDH used as endogenous reference.
RCR data were analyzed using comparative ΔΔCt method. If not specified, GAPDH used as endogenous reference.
3
HRV72 Infection Transcriptome Analysis in A549 Cells
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The A549 cells grown in 25 cm2 culture flasks were infected with HRV72 at multiplicity of infection (MOI) of 10 or mock-infected at three independent replicates with a week interval [24 (link)]. Total mRNA was extracted from both HRV72-infected and mock-infected A549 cells using GeneJET RNA purification kit (Thermo Fisher Scientific Inc., Germany), according to the manufacturer’s instructions. DNA contamination was removed using DNase I treatment (Worthington Biochemical Corporation). RNA concentration (at 260 nm) and purity (260/280 nm and 260/230 nm ratio) was measured by using a Thermo Scientific NanoDrop 1000 Spectrophotometer. The RNA integrity and DNA removal was confirmed by 1% denaturating agarose gel electrophoresis. The proportion of the full-length RNA was evaluated by microfluidic analysis using Agilent 2100 Bioanalysier using RNA LabChip Kit (Germany), as per manufacturer’s instructions. The samples with RNA Integrity Number (RIN) of 7 and greater were used for microarray hybridization.
4
Transcriptome Analysis of MDCK Cells
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Total RNA was isolated from the tenth generation of MDCK cells with CPV-LZ1 infection using TRIzol reagent (Life Technologies) following the manufacture’s instruction. The uninfected F10 MDCK cells act as mock control. The RNA quality was checked using a NanoVue UV spectrophotometer (Thermo Scientific, Rockford, IL, USA). Qualified total RNA was further purified by RNA LabChip kit (Agilent Technologies, Santa Clara, CA, USA).
Samples RNA was amplified using a GeneChip 3‘IVT Express Kit (Affymetrix, Cleveland, OH, USA) to generate first strand cDNA and second strand cDNA, respectively. Then complementary RNA (cRNA) was produced and labeled using GeneChip HT IVT Labeling Kit (Affymetrix). The labeled cRNA was purified and quality test by an Agilent RNA 6000 Nano Kit (Agilent Technologies), followed by processed for microarray analysis on an Affymetrix Canine Genome 2.0 Array (Affymetrix) using a GeneChip Hybridization, Wash, and Stain Kit (Affymetrix), according to the manufacturer’s instructions. Arrays were scanned by an Affymetrix GeneChip Scanner 3000 System (Affymetrix). The raw data were normalized by Range Migration Algorithm and further analyzed by Affymetrix Microarray Suite Algorithm (MAS5).
Samples RNA was amplified using a GeneChip 3‘IVT Express Kit (Affymetrix, Cleveland, OH, USA) to generate first strand cDNA and second strand cDNA, respectively. Then complementary RNA (cRNA) was produced and labeled using GeneChip HT IVT Labeling Kit (Affymetrix). The labeled cRNA was purified and quality test by an Agilent RNA 6000 Nano Kit (Agilent Technologies), followed by processed for microarray analysis on an Affymetrix Canine Genome 2.0 Array (Affymetrix) using a GeneChip Hybridization, Wash, and Stain Kit (Affymetrix), according to the manufacturer’s instructions. Arrays were scanned by an Affymetrix GeneChip Scanner 3000 System (Affymetrix). The raw data were normalized by Range Migration Algorithm and further analyzed by Affymetrix Microarray Suite Algorithm (MAS5).
5
Dietary Impacts on Fish Tissues
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Liver, midgut and hindgut from eighteen individual fish per dietary treatment were homogenized in 1 ml of TriReagent® (Sigma-Aldrich, Dorset, UK), total RNA isolated following manufacturer’s instructions, and quantity and quality determined by spectrophotometry using a Nanodrop ND-1000 (Labtech Int., East Sussex, UK) and electrophoresis using 200 ng of total RNA in a 1% agarose gel. Additionally the Agilent Bioanalyzer with the RNA LabChip kit (Agilent Technologies) was used to analyze approximately 300 ng of total RNA from a randomly selected number of samples (72 samples; 12 samples per treatment and tissue) and provide an RNA integrity number (RIN), which was higher than 8.0 in all samples (average RIN = 8.2). cDNA was synthesized as detailed in [20 (link)] and samples pooled to obtain n = 6 per dietary treatment.
6
RNA Sequencing of Fungal Cultures
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Following 36 and 48 h incubation, total RNA was extracted from each culture according to a standard phenol/chloroform method (Brasileiro et al., 2015 ). Mycelia from liquid media was collected by filtration with Whatman® filter paper n°1, whilst from semi-solid cultures mycelia from the surface of each agar plate was collected manually using a sterilized spatula. Extracted total RNA was quantified and integrity determined using an Agilent 2100 Bioanalyzer and RNA LabChip® kit system (Agilent Technologies, Santa Clara, CA, USA). Isolation of mRNA, cDNA library construction and Illumina RNA-seq were conducted by Eurofins MWG Operon (Louisville, KY, USA). All treatments from the replicate bioassays were paired-end sequenced (2 × 100 bases) using TruSeq RNA Chemistry v3 on two flow cell channels of an Illumina Hiseq2000 system (Illumina Inc., San Diego CA, USA).
7
Transcriptome Analysis of PRKN Mutations
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RNA was extracted from blood of PRKN biallelic and monoallelic mutation carriers (PRKN/all) (n = 23, mean age ± SD: 56.2 ± 13.2, mean AAO ± SD: 38.8 ± 18.2) and controls (n = 6, mean age ± SD: 71.7 ± 9.1) with RNeasy Qiagen Minikit and DNase I digested before assessing the concentration, quality and RNA integrity with Agilent 2100 bioanalyser, RNA LabChip kit and associated software (Agilent). AmpliseqTM whole transcriptome analysis was performed with the Ion Proton (Life Technologies, Inc.) with average of 9.96 M ± 1.14 M reads. Transcriptome reads were aligned to the GRCh37/hg19 reference genome and analysed by RNA-seq Analysis plugin (v.5.0.0.2) using default analysis settings. The DESeq2 R44 (link) package (v.1.18.1) in Bioconductor was used to test for differential expression by use of negative binomial generalized linear models; the estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions. The non-normalized counts of sequencing reads/fragments were used in DESeq2’s statistical model that accounts for library size differences internally. Differentially expressed genes (DEGs) with nominally significant P-values (<0.05) and log2-fold (L2F) changes (>|0.2|) were mapped on KEGG pathways with pathview.44 (link)
8
Transcriptome Analysis of Heart Tissue
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After 12 weeks of treatment, the total RNA was isolated from the heart tissue using Trizol reagent (Invitrogen, CA, United States). Determine the concentration of total RNA by fluorescence-based quantitation using an RNA RiboGreen® dye assay (e.g., Quant-iT™ RiboGreen® RNA Reagent and Kit) and the NanoDrop Fluorospectrometer for initial RNA concentration of 5 pg/μL to 1 ng/μL (www.nanodrop.com ). RNA integrity was tested using the Agilent 2,100 Bioanalyzer with an RNA LabChip Kit. Global transcriptome analysis of total RNA (50 ng/μl) was performed using the Affymetrix GeneChip Primeview™, according to the manufacturer’s instructions. Hybridization, staining, normalization and data analysis were performed following the standard protocol established by Agilent Technologies, Inc.
9
Transcriptome Profiling of Primary Sjögren's Syndrome
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Total RNA was extracted from eight samples (four pSS and four control subjects) using TRIzol reagent (Life Technologies, Carlsbad, CA, USA). The RNeasy Mini Kit (Qiagen, GmBH, Hilden, Germany) was used to purify the total RNA according to the manufacturer’s recommendation. Purified total RNA was quantified using a NanoDrop 1000 (Thermo Fisher Scientific, Waltham, MA, USA). The assessment of RNA integrity was determined using RNA LabChip™ kits and an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Only samples with 2100 RIN ≥7.0 and 28S/18S ≥0.7 were used.
Agilent SurePrint G3 microarray was used to investigate 63,431 lncRNAs and 39,887 mRNAs. Total RNA was amplified and labeled using a Low Input Quick Amp Labeling Kit, One-Color (Agilent Technologies, Santa Clara, CA, US). Labeled cRNA were purified using an RNeasy Mini Kit (Qiagen, GmBH, Hilden, Germany). The microarray hybridization was performed based on the manufacturer’s standard protocols (Agilent Technologies, Santa Clara, CA, US). Slides were washed in staining dishes and scanned. Raw data were normalized using a Quantile algorithm in Gene Spring Software 11.0 (Agilent Technologies, Santa Clara, CA, US).
Agilent SurePrint G3 microarray was used to investigate 63,431 lncRNAs and 39,887 mRNAs. Total RNA was amplified and labeled using a Low Input Quick Amp Labeling Kit, One-Color (Agilent Technologies, Santa Clara, CA, US). Labeled cRNA were purified using an RNeasy Mini Kit (Qiagen, GmBH, Hilden, Germany). The microarray hybridization was performed based on the manufacturer’s standard protocols (Agilent Technologies, Santa Clara, CA, US). Slides were washed in staining dishes and scanned. Raw data were normalized using a Quantile algorithm in Gene Spring Software 11.0 (Agilent Technologies, Santa Clara, CA, US).
10
Myocardial Infarction in Fat-1 Transgenic Mice
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The infarcted parts of myocardium, the border zone of infarct scars, and the remote zone of noninfarcted myocardium from infarcted fat‐1 transgenic mice (n = 3) and infarcted WT mice (n = 3) were used for RNA (50%) and protein extraction (50%).
Total RNA was isolated using kits according to manufacturer's instructions. For detecting the microRNA expression, miRcute miRNA isolation kit, miRcute miRNA First‐Strand cDNA synthesis kit and miRcute miRNA qPCR detection kit (SYBR Green) were used (all from Vazyme Biotech Co. Ltd, Nanjing, China). For detecting mRNA, TRIzol RNA (Invitrogen, Carlsbad, CA, USA), ThermoScript™ RT‐PCR system and a Fast Start universal SYBR green master (ROX) were used. RNA quality and integrity were determined using a 2100 bioanalyzer (Agilent Technologies Inc) and RNA LabChip® kits (Agilent Technologies Inc).
Total RNA was isolated using kits according to manufacturer's instructions. For detecting the microRNA expression, miRcute miRNA isolation kit, miRcute miRNA First‐Strand cDNA synthesis kit and miRcute miRNA qPCR detection kit (SYBR Green) were used (all from Vazyme Biotech Co. Ltd, Nanjing, China). For detecting mRNA, TRIzol RNA (Invitrogen, Carlsbad, CA, USA), ThermoScript™ RT‐PCR system and a Fast Start universal SYBR green master (ROX) were used. RNA quality and integrity were determined using a 2100 bioanalyzer (Agilent Technologies Inc) and RNA LabChip® kits (Agilent Technologies Inc).
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