Paxgene blood rna tube

Manufactured by BD

Sourced in United States, Canada, Germany, France, United Kingdom, Switzerland

The PAXgene Blood RNA tubes are a product designed to collect and stabilize RNA from whole blood samples. The tubes contain a proprietary reagent that immediately protects the RNA from degradation upon blood collection, allowing for reliable RNA analysis.

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Lab products found in correlation

137 protocols using paxgene blood rna tube

Whole Blood RNA Extraction and Analysis

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RNA was prepared from whole blood collected and stored in PAXgene Blood RNA Tubes (BD, Heidelberg, Germany) using the PAXgene Blood miRNA Kit (Qiagen, Hilden, Germany). Isolation of RNA was performed using a QIAcube according to protocols provided by the manufacturer Qiagen. Purity and concentration of RNA were determined using a NanoDrop ND-1000 UV-Vis Spectrophotometer (Thermo Scientific, Hennigsdorf, Germany). To ensure a consistently high RNA quality, all preparations were analyzed using RNA 6000 Nano LabChips on a 2100 Bioanalyzer (both from Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer's instructions. Samples exhibiting a RNA integrity number (RIN) less than seven were excluded from subsequent analyses. The Illumina TotalPrep-96 RNA Amplification Kit (Ambion, Darmstadt, Germany) was used for reverse transcription of 500 ng RNA into double-stranded (ds) cDNA and subsequent synthesis of biotin-UTP-labeled antisense-cRNA using this cDNA as the template. Finally, in total 3,000 ng of cRNA were hybridized with a single array on the Illumina HumanHT-12 v3 BeadChips, followed by washing and detection steps in accordance with the Illumina protocol. BeadChips were scanned using the Illumina Bead Array Reader. Further details on expression data transformation and quality control are available elsewhere [11 (link)].

Haring R., Schurmann C., Homuth G., Steil L., Völker U., Völzke H., Keevil B.G., Nauck M, & Wallaschofski H. (2015). Associations between Serum Sex Hormone Concentrations and Whole Blood Gene Expression Profiles in the General Population. PLoS ONE, 10(5), e0127466.

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Standardized Serum and Tissue Collection

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In order to minimize variability derived from sample collection and handling, a standard procedure was developed that was strictly adhered to for all sample collection and processing steps. After blood withdrawal, serum tubes were left at room temperature for 1 hour; samples were then centrifuged for 15 min at 2000 rpm (750 g) at room temperature. Subsequently the serum was removed, aliquoted, snap-frozen and stored at −80°C until RNA extraction. Whole blood was collected in PAXgene Blood RNA tubes (BD Biosciences) according to the manufacturer's instructions and stored at −80°C until RNA extraction. Primary melanoma, melanoma metastasis, as well as the corresponding healthy skin were excised and immediately stored at –80°C until further use. Staging of diseases was performed by the histology departments of the respective clinics.

Margue C., Reinsbach S., Philippidou D., Beaume N., Walters C., Schneider J.G., Nashan D., Behrmann I, & Kreis S. (2015). Comparison of a healthy miRNome with melanoma patient miRNomes: are microRNAs suitable serum biomarkers for cancer?. Oncotarget, 6(14), 12110-12127.

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RNA-seq Analysis of Whole Blood

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Whole blood was collected into PAXgene Blood RNA tubes (PreAnalytiX GmbH– BD Biosciences, Mississauga, ON, Canada), and RNA isolated. The quality and yield of the isolated RNA was determined with an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) prior to RNA-sequencing (Illumina HiSeq4000 Sequencing). Transcript differential expression analysis was performed with DESeq.

Barrett T.J., Schlegel M., Zhou F., Gorenchtein M., Bolstorff J., Moore K.J., Fisher E.A, & Berger J.S. (2019). Platelet regulation of myeloid suppressor of cytokine signaling 3 accelerates atherosclerosis. Science translational medicine, 11(517), eaax0481.

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Standardized Blood Sterol Measurements

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A blood sample was drawn into PaxGene Blood RNA tubes (BD Biosciences, San Joes, CA), which contain 6.9 ml of RNA stabilization additive to which a maximum of 2.5 ml of blood can be added. Therefore, all analyses were corrected for a dilution factor of 3.8. Since the amount of blood collected per tube varied, we normalized sterol metabolites to free cholesterol levels measured in the same samples. Tubes were frozen and stored at −20°C.
A number of controls were carried out to ensure accuracy of measurements. First, a potential interference of the RNA stabilization additive with the measurements of sterol levels was examined. No effect on 7DHC measurements were observed, but desmosterol and lanosterol levels were reduced by approximately 50%. Second, storage effects were tested in 117 sample aliquots measured in 2014 and 2016, and no significant differences were observed (supplemental figure 1). Both measurements for each sample were averaged in the final analysis.

Korade Ž., Liu W., Warren E.B., Armstrong K., Porter N.A, & Konradi C. (2017). Effect of psychotropic drug treatment on sterol metabolism. Schizophrenia research, 187, 74-81.

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PKAN Patient Blood RNA Analysis

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Informed consent was obtained from all subjects, and the experiments conformed to the principles set out in the WMA Declaration of Helsinki and the Department of Health and Human Services Belmont Report. All subjects were consented as part of OHSU's IRB‐approved protocol e7232 with additional work covered by protocol e144. Human blood from PKAN patients and age‐matched controls was collected using PAXgene^® Blood RNA tubes (BD Biosciences). After a 24‐h incubation to ensure lysis of red blood cells, remaining cells were pelleted and stored at −80°C. Later, total RNA was isolated (Qiagen) and analyzed using qRT–PCR method.

Jeong S.Y., Hogarth P., Placzek A., Gregory A.M., Fox R., Zhen D., Hamada J., van der Zwaag M., Lambrechts R., Jin H., Nilsen A., Cobb J., Pham T., Gray N., Ralle M., Duffy M., Schwanemann L., Rai P., Freed A., Wakeman K., Woltjer R.L., Sibon O.C, & Hayflick S.J. (2019). 4′‐Phosphopantetheine corrects CoA, iron, and dopamine metabolic defects in mammalian models of PKAN. EMBO Molecular Medicine, 11(12), e10489.

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COVID-19 Longitudinal Biomarkers of Lung Injury

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Between March 2020 and February 2021, the prospective observational “COVID-19 Longitudinal Biomarkers of Lung Injury” (COLOBILI) study consented and enrolled 42 ICU adult (>18 years) patients with respiratory deterioration from suspected COVID-19 at St. Michael’s Hospital (Toronto, Canada) (Table 1). Whole blood (2.5 mL) was drawn into PaxGene Blood RNA tubes (BD Biosciences) at admission (Day 1, D1) and Day 7 (D7) in the ICU. After enrollment, 20 patients were identified to be SARS-CoV-2 PCR positive (but blood culture negative at both timepoints), and the remaining 22 SARS-CoV-2 PCR negative patients had ≥2 negative PCR tests. All patients satisfied Sepsis-3 criteria for sepsis (suspected/confirmed infection with a SOFA score ≥2 at ICU admission) (4 (link)). After the second blood draw, nine patients (4 SARS-CoV-2 positive, 5 negative) died within 28 days in the ICU. Samples were frozen and transported to Vancouver, Canada, for RNA extraction (PAXgene Blood RNA Kit; Qiagen) followed by RNA-Seq. Whole blood from 5 healthy controls from Vancouver, Canada were processed alongside the patient samples. Further details on study design and RNA-Seq methodology can be found in our previously published protocol (11 (link)).

An A.Y., Baghela A., Zhang P., Falsafi R., Lee A.H., Trahtemberg U., Baker A.J., dos Santos C.C, & Hancock R.E. (2023). Persistence is key: unresolved immune dysfunction is lethal in both COVID-19 and non-COVID-19 sepsis. Frontiers in Immunology, 14, 1254873.

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Peripheral Blood RNA Extraction

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Blood samples were collected using PAXgene® Blood RNA tubes (BD Biosciences) as per manufacturer protocol and stored at −80°C until the day of RNA extraction. Total RNA was extracted from peripheral blood samples using a commercially available extraction kit (PAXgene Blood RNA Kit; QIAGEN). Photometric control of RNA quantity and purity was performed by measuring ultraviolet absorbance at different wavelengths to monitor contamination with proteins (Abs 260/280 nm ratio) or other organic compounds (Abs 260/230 nm ratio). A total of 100 ng total RNA per sample was used for miRNA expression studies.

Steinberg C., Gaudreault N., Papadakis A.I., Henry C., Champagne J., Philippon F., O’Hara G., Blier L., Plourde B., Nault I., Roy K., Sarrazin J.F., Spatz A, & Bossé Y. (2023). Leucocyte-derived micro-RNAs as candidate biomarkers in Brugada syndrome. Europace, 25(6), euad145.

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Longitudinal Blood RNA and Serum Sampling

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Blood was collected in PAXgene® Blood RNA tubes (BD Biosciences) for subsequent RNA extraction just before vaccine administration (T0H), 4 h after (T4H) and 24 h after (T24H). For serum collection, blood was collected at T0, and every 2 weeks during 1 year (Fig. 1a).

Jouneau L., Lefebvre D.J., Costa F., Romey A., Blaise-Boisseau S., Relmy A., Jaszczyszyn Y., Dard-Dascot C., Déjean S., Versillé N., Guitton E., Hudelet P., Curet M., De Clercq K., Bakkali-Kassimi L., Zientara S., Klonjkowski B, & Schwartz-Cornil I. (2020). The antibody response induced FMDV vaccines in sheep correlates with early transcriptomic responses in blood. NPJ Vaccines, 5, 1.

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Analysis of Gene Expression in PBCs

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For analysis of gene expression in PBCs, 2.5 ml samples of whole-blood were collected in PAXgene blood RNA tubes (BD, Franklin Lakes, NJ) at the same time as serum samples. Total RNA was isolated from these tubes using a PAXgene blood RNA kit (Qiagen, Valencia, CA) according to manufacturer’s specifications and quantified using a Thermo Scientific NanoDrop Lite Spectrophotometer (Thermo Fisher Scientific, MA, USA). cDNA was obtained using a High-Capacity RNA-to-cDNA kit (Thermo Fisher Scientific, Foster City, CA, USA) for further analysis. Transcripts of Klotho gene (KL), TNF, IL6, IL10, and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) as constitutive gene, were measured by real-time TaqMan quantitative PCR (qRT-PCR) with TaqMan Fast Universal PCR master mix (Thermo Fisher Scientific) in a 7500 Fast Real-Time PCR System (Thermo Fisher Scientific). TaqMan gene expression assays for each transcript were: Hs00183100_m1 [KL], Hs00174128_ml [TNF], Hs00985639_ml [IL6], Hs0961622_m1 [IL10], and Hs99999905_m1 [GAPDH]. The level of target mRNA was estimated by relative quantification using the comparative method (2^−ΔΔCt) by normalizing to GAPDH expression. mRNA levels were expressed as arbitrary units (a.u.). Quantification of each cDNA sample was tested in triplicate. A corresponding non-reverse transcriptase reaction was included as a control for DNA contamination.

Donate-Correa J., Ferri C.M., Martín-Núñez E., Pérez-Delgado N., González-Luis A., Mora-Fernández C, & Navarro-González J.F. (2021). Klotho as a biomarker of subclinical atherosclerosis in patients with moderate to severe chronic kidney disease. Scientific Reports, 11, 15877.

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Interferon Gene Signature Measurement

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The IFNGS was determined using a previously validated four gene score by assessing the levels of IFI27, IFI44, IFI44L, and RSAD2 through quantitative polymerase chain reaction (q-PCR) using TaqMan gene expression assay (ThermoFisher Scientific, Inc.) from subjects’ whole blood [14 , 15 (link)]. Peripheral blood was collected by venipuncture in PAXgene Blood RNA tubes (BD Diagnostics, Inc) and stored at −20°C. RNA was isolated using PAXgene Blood RNA Kit (Qiagen, Inc.) following manufacturer’s instructions. Reverse Transcription Supermix for RT-qPCR by iScript (Bio-Rad, Inc) was used to synthesize cDNA. Expression level of GAPDH was used as housekeeping gene to normalize gene expression. ∆∆C_t was calculated by subtracting the mean determined from a set of healthy controls (n=30) for that particular gene. An IFN score was calculated as the average of the fold inductions for the 4 genes. High IFN score was determined as subjects with IFNGS above the two-SD of the mean of the healthy controls.

Hasni S., Gupta S., Davis M., Poncio E., Temesgen-Oyelakin Y., Joyal E., Fike A., Manna Z., Auh S., Shi Y., Chan D., Carlucci P., Biehl A., Dema B., Charles N., Balow J., Waldman M., Siegel R., Kaplan M, & Rivera J. (2019). Safety and Tolerability of Omalizumab, A Randomized Clinical Trial of Humanized anti-IgE Monoclonal Antibody in Systemic Lupus Erythematosus (STOP LUPUS).. Arthritis & rheumatology (Hoboken, N.J.), 71(7), 1135-1140.

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