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Rna 6000 pico labchip

Manufactured by Agilent Technologies
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The RNA 6000 Pico LabChip is a microfluidic-based electrophoresis system designed for the analysis of small quantities of RNA samples. It enables rapid, automated, and sensitive quantification and sizing of RNA molecules in a simple, easy-to-use platform.

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Lab products found in correlation

Agilent 2100 bioanalyzer, by Agilent Technologies (15 mentions) Trizol reagent, by Thermo Fisher Scientific (6 mentions) Nanodrop, by Thermo Fisher Scientific (5 mentions) Rneasy mini kit, by Qiagen (4 mentions) Dnase 1, by Thermo Fisher Scientific (3 mentions) Tri reagent, by Merck Group (2 mentions) Nanodrop 2000, by Thermo Fisher Scientific (2 mentions) Micropoly a purist kit, by Thermo Fisher Scientific (2 mentions) 2100 bioanalyzer, by Agilent Technologies (2 mentions) Nanodrop 1000 spectrophotometer, by Thermo Fisher Scientific (2 mentions) Agilent 2100 bioanalyser, by Agilent Technologies (2 mentions) Hiseq 2000, by Illumina (2 mentions) Trizol, by Thermo Fisher Scientific (2 mentions) Nanodrop spectrophotometer, by Thermo Fisher Scientific (2 mentions) Direct zol kit, by Zymo Research (1 mentions) Wt ovation one direct amplification system, by Tecan (1 mentions) Du 730 life science uv vis spectrophotometer, by Beckman Coulter (1 mentions) Proteinase k, by Qiagen (1 mentions) Rna storage solution, by Thermo Fisher Scientific (1 mentions) Nanodrop nd 1000, by Isogen Life Science (1 mentions)

Close spelling variants of this product

RNA 6000 Pico LabChip kit (33 citations) RNA 6000 Pico (19 citations) RNA 6000 Nano/Pico LabChip (5 citations) RNA 6000 Pico LabChip reagent set (4 citations) Bioanalyzer RNA 6000 Pico LabChip (3 citations) Agilent RNA 6000 Pico LabChip (2 citations)

23 protocols using rna 6000 pico labchip

1

Neutrophil RNA Microarray Analysis

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Total RNA was extracted from purified neutrophil populations using the Direct-zol kit (Zymo Research, Irvine, CA). RNA purity and concentration were determined spectrophotometrically. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) using an RNA 6000 Pico LabChip. Total RNA was amplified and labeled using the Nugen Ovation Pico WTA System V2 kit (Tecan Genomics, Redwood City, CA). Affymetrix (Santa Clara, CA) GeneChip Mouse Genome 430 2.0 microarray processing was carried out as outlined in the Affymetrix GeneChip manual. Data capture and initial array quality assessment were performed with the GeneChip operating software. The R statistical analysis tool was used to calculate probe-level summaries (frozen robust multiarray average analysis) from the array CEL files (30 ). All analyses were conducted using R. Pairwise group assessments were conducted for each probeset using a Student’s or Welch’s t test depending on the results of a Bartlett’s test for equal variance. Genes were considered differentially expressed if they displayed a fold change >1.5 and unadjusted P < 0.05.
Thanabalasuriar A., Chiang A.J., Morehouse C., Camara M., Hawkins S., Keller A.E., Koksal A.C., Caceres C.S., Berlin A.A., Holoweckyj N., Takahashi V.N., Cheng L., de los Reyes M., Pelletier M., Patera A.C., Sellman B., Hess S., Marelli M., Boo C.C., Cohen T.S, & DiGiandomenico A. (2021). PD-L1+ neutrophils contribute to injury-induced infection susceptibility. Science Advances, 7(10), eabd9436.
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2

Amplification and Quality Evaluation of Total RNA

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Total RNA was amplified from each sample using the WT-Ovation™ One-Direct Amplification System (NuGEN) according to the manufacturer’s directions. The use of an aluminum cooling block on ice facilitated the handling of the reaction tubes. The amplified cDNA products passed the purity test of showing Abs260/Abs280 ratios between 1.9 to 2.0, and a subset was analyzed on an Agilent Bioanalyzer using the RNA 6000 Pico LabChip with the mRNA Pico program to assess size distribution as previously described [13 ]. Post-SPIA modification and post-amplification work was performed in a separate workspace.
Chéry L., Lam H.M., Coleman I., Lakely B., Coleman R., Larson S., Aguirre-Ghiso J.A., Xia J., Gulati R., Nelson P.S., Montgomery B., Lange P., Snyder L.A., Vessella R.L, & Morrissey C. (2014). Characterization of single disseminated prostate cancer cells reveals tumor cell heterogeneity and identifies dormancy associated pathways. Oncotarget, 5(20), 9939-9951.
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3

RNA Extraction and Quality Analysis

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From individual GC samples, total RNA was purified using a combination of Tri Reagent (Sigma-Aldrich, St. Louis, MO, USA) and the RNeasy Mini Kit (Qiagen, Hilden, Germany). For each sample, the quality of the purified RNA was analyzed using an Agilent 2100 Bioanalyzer and an RNA 6000 Pico LabChip (RNA 6000 Pico assay kit, Agilent Technologies, Waldbronn, Germany). The RNA integrity number should be higher than the internal threshold value in order to qualify samples for the study. Total RNA quantity in each sample was measured using a Beckman Coulter Du730 life science UV/vis spectrophotometer.
Kristensen S.G., Mamsen L.S., Jeppesen J.V., Bøtkjær J.A., Pors S.E., Borgbo T., Ernst E., Macklon K.T, & Andersen C.Y. (2018). Hallmarks of Human Small Antral Follicle Development: Implications for Regulation of Ovarian Steroidogenesis and Selection of the Dominant Follicle. Frontiers in Endocrinology, 8, 376.
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4

Plasma RNA Extraction and Integrity

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After collection EDTA blood samples (5 ml) were immediately placed on ice. Blood samples were centrifuged twice at 1700 rpm for 20 min at 4°C and plasma was collected in cryovials for storage at −80°C until use. After thawing an 75 μl aliquot of plasma was added to 2 ml of TriReagent (Sigma Aldrich) and passed through a 20 gauge-needle for about 10 times. Then, proteinase K (Qiagen) was added to each sample with a final concentration of 0.05 mg/ml and samples were digested for 45 min at 56°C. Following incubation, each sample was passed through a 20 gauge-needle for about 10 times and centrifuged at 4000 rpm for 10 minutes at 4°C.
RNA extraction was then performed through the Qiagen RNeasy mini kit according to the manufacturer instructions. RNA was eluted in 30 μl of RNase free water.
To assess RNA integrity 1 μl of total RNA was analyzed through the Agilent 2100 Bioanalyzer and the RNA 6000 Pico LabChip, according to the manufacturer instruction. Electropherograms showed trace of RNA samples that could not be quantified, characterized by high fragmentation.
Galdiero F., Romano A., Pasquinelli R., Pignata S., Greggi S., Vuttariello E., Bello A.M., Calise C., Scaffa C., Pisano C., Losito N.S., Fusco A., Califano D, & Chiappetta G. (2015). Detection of high mobility group A2 specific mRNA in the plasma of patients affected by epithelial ovarian cancer. Oncotarget, 6(22), 19328-19335.
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5

Total RNA Extraction and mRNA Purification

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Each frozen sample was ground in a mortar with liquid nitrogen, and then total RNA was isolated using TRIzol reagent (Invitrogen, USA) following the manufacture's protocol. The final total RNA was dissolved in 200 µL RNase-free water. The concentration of total RNA was determined using a NanoDrop2000 spectrophotometer (Thermo Scientific, USA), and the RNA integrity was checked using an RNA 6000 Pico LabChip with the Agilent 2100 Bioanalyzer (Agilent, USA). The total RNA was incubated with 10 U DNase I (Ambion, USA) at 37°C for 1 h, and then nuclease-free water was added to dilute the sample volume to 250 µL. The messenger RNA (mRNA) was further purified with a MicroPoly(A) Purist Kit (Ambion, USA) according to the manufacturer's protocol. The mRNA was dissolved in 100 µL of RNA Storage Solution (Ambion). The final concentration was determined using a NanoDrop2000 spectrophotometer.
Wang W., Wu X., Liu Z., Zheng H, & Cheng Y. (2014). Insights into Hepatopancreatic Functions for Nutrition Metabolism and Ovarian Development in the Crab Portunus trituberculatus: Gene Discovery in the Comparative Transcriptome of Different Hepatopancreas Stages. PLoS ONE, 9(1), e84921.
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6

RNA Extraction from Frozen Tumor Samples

Cited 2 times
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RNA isolation was performed as described previously [15] (link). In short, approximately 30 mg of frozen tumor was disrupted/lysed and homogenized and total RNA was isolated and treated with DNase using the RNeasy mini kit (Qiagen, The Netherlands) according to the manufacturer's protocol. Quantity and integrity were assessed with the Bioanalyzer Agilent BioAnalyzer-2100 (Bioanalyzer, Agilent Technologies, Santa Clara, CA) in combination with an RNA 6000 Pico-LabChip. The average RNA integrity number 8.5 (range: 7.2–9.8) was found to be appropriate [22] (link). RNA concentration was quantified using a NanoDrop ND-1000 (Isogen Life Science) spectrophotometer.
Boerkamp K.M., van Steenbeek F.G., Penning L.C., Groot Koerkamp M.J., van Leenen D., Vos-Loohuis M., Grinwis G.C, & Rutteman G.R. (2014). The Two Main Forms of Histiocytic Sarcoma in the Predisposed Flatcoated Retriever Dog Display Variation in Gene Expression. PLoS ONE, 9(6), e98258.
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7

RNA-Seq Analysis of Sorted Human Neutrophils

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Total RNA from FACS sorted human neutrophils was extracted using an Arcturus PicoPure RNA isolation kit (Thermo Fisher Scientific, Waltham, MA) according to the manufacturer’s instructions. The quality of total RNA from neutrophils was assessed with a 2100 Bioanalyzer using a RNA 6000 Pico LabChip (Agilent Technologies, Santa Clara, CA). RNA for which the RNA integrity number (RIN) was greater than 7.0 was used for library preparation and RNA-Sequencing (RNA-Seq). RNA-Seq was performed by the NextSeq 500 system (Illumina, San Diego, CA) according to the manufacturer’s instructions. FASTQ sequence data was trimmed and filtered by fastp (v0.21.0), was aligned by HISAT2 (v2.1.0) and then the expression levels were calculated by StringTie (v2.1.3) using Subio platform ver. 1.24 (Subio Inc., Kagoshima, Japan). The count data were log 2 transformed, normalized by global normalization, centered and then analyzed using Subio Platform. Gene ontology (GO) enrichment analysis was performed by g:Profiler. GO associated with up-regulated genes in NP neutrophils was identified based on an adjusted p value <0.05 by g:SCS algorithm.15 (link) We also used the TPM (transcripts per million) data for individual comparison of each gene.
Poposki J.A., Klingler A.I., Stevens W.W., Suh L.A., Tan B.K., Peters A.T., Abdala-Valencia H., Grammer L.C., Welch K.C., Smith S.S., Conley D.B., Kern R.C., Schleimer R.P, & Kato A. (2021). Elevation of activated neutrophils in chronic rhinosinusitis with nasal polyps. The Journal of allergy and clinical immunology, 149(5), 1666-1674.
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8

Single-cell RNA-seq of FFPE samples

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Total RNA was extracted from the pooled LCM-captured cells with the NucleoSpin totalRNA FFPE XS kit (Macherey-Nagel, REF740969) with minor modifications. In short, cells in the cap were covered with lysis buffer, incubated at 56°C for 15 min and then spun down. Extracted RNA was bound onto the column with binding buffer and genomic DNA was digested for 15 min in rDNase incubation solution. After two washes, RNA was eluted with 10 μl of RNase-free water. rRNA was removed from the purified RNA with the Ribo-Zero Magnetic Gold Kit (Epicentre, MRZG126). The purified RNA was amplified with the SMARTer Universal Low Input RNA Kit for Sequencing (Clontech, 634938) and libraries were generated with the Low Input Library Prep Kit (Clontech, 634947). Libraries were sequenced on an Illumina HiSeq2000 (100 PE bp) at the Welgene Biotech Company, which generated 6 Gb of data per sample. RNA was quantified and qualitated with the Bioanalyzer 2100 (Agilent Technologies) using a RNA 6000 Pico LabChip (Agilent, 5065–4401). DNA was quantified and qualitated with an Agilent 2200 TapeStation system using High Sensitivity D1000 ScreenTape (Agilent, 5067–5584) and High Sensitivity D1000 Reagents (Agilent, 5067–5585).
Lin C.Y., Huang S.C., Tung C.C., Chou C.H., Gau S.S, & Huang H.S. (2016). Analysis of Genome-Wide Monoallelic Expression Patterns in Three Major Cell Types of Mouse Visual Cortex Using Laser Capture Microdissection. PLoS ONE, 11(9), e0163663.
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9

Shotgun Sequencing Library Preparation

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Approximately 5 µg of the amplified cDNA library was sheared by nebulisation at 200 kPa for 2 min. The concentration and integrity of the nebulised cDNA sample was determined using a Bioanalyzer 2100, with a DNA 12000 Labchip (Agilent, Santa Clara, USA) according to manufacturer's instructions. The GS-FLX titanium shotgun sequence library was then prepared following the manufacturer's instructions (Roche Diagnostics, Basel, Switzerland). The quality of sequencing library was then assessed using a Bioanalyzer 2100, fitted with an RNA 6000 Pico Lab Chip (Agilent) according to the manufacturer's instructions. Quantification of the sequence library was performed using quantitative real-time PCR. Emulsions were prepared using the Large Volume Emulsion PCR Kit (Roche Diagnostics). Finally, enriched beads were loaded onto one half of a picotitre plate for sequencing following the manufacturer's protocol.
Giordano A., Cogan N.O., Kaur S., Drayton M., Mouradov A., Panter S., Schrauf G.E., Mason J.G, & Spangenberg G.C. (2014). Gene Discovery and Molecular Marker Development, Based on High-Throughput Transcript Sequencing of Paspalum dilatatum Poir. PLoS ONE, 9(2), e85050.
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10

Neuronal Gene Expression Analysis by LCM

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Gene expression analysis was performed on neurones isolated from 10 cases (5 high neuronal DDR and 5 low DDR) using laser capture microscopy (LCM) (Figure 1), based on previous investigation of the neuronal DDR (DNA–PKcs and γH2AX) in this cohort [8]. Details of cases used in the microarray study are shown in Table 1. Validation experiments were performed on LCM‐isolated neurones from the remaining 29 CFAS cases. Frozen sections (7 μm) were fixed in ice cold acetone for 3 min and stained with Toludine Blue for 1 min. Sections were dehydrated in a graded series of ethanol (70, 95 and 100%), extensively cleared in xylene and air dried for 1 h. Approximately, 1000 pyramidal neurones were isolated from each case using a PixCell II LCM system (Life Technologies, Paisley, UK). Total RNA was extracted using the PicoPure RNA extraction kit according to the manufacturer's protocol (Life Technologies), with typical yields of 100 ng of RNA. The quantity (NanoDrop 1000 spectrophotometer, Thermo Scientific, Wilmington, DE USA) and quality (Agilent Bioanalyser 2100, RNA 6000 Pico LabChip; Agilent, Palo Alto, CA, USA) of the starting RNA were analysed. Sterile solutions made with diethylpyrocarbonate (DEPC)‐treated water and RNAse‐free conditions were used throughout this protocol.
Simpson J.E., Ince P.G., Minett T., Matthews F.E., Heath P.R., Shaw P.J., Goodall E., Garwood C.J., Ratcliffe L.E., Brayne C., Rattray M, & Wharton S.B. (2015). Neuronal DNA damage response‐associated dysregulation of signalling pathways and cholesterol metabolism at the earliest stages of Alzheimer‐type pathology. Neuropathology and Applied Neurobiology, 42(2), 167-179.
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