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Paxgene blood rna tubes

Manufactured by Thermo Fisher Scientific
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The PAXgene Blood RNA Tubes are designed to stabilize RNA in whole blood samples, allowing for the collection, transport, and storage of RNA for subsequent gene expression analysis. The tubes contain a proprietary reagent that immediately interacts with the blood to prevent ex vivo changes in the RNA profile.

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Lab products found in correlation

Magmax for stabilized blood tubes rna isolation kit, by Thermo Fisher Scientific (4 mentions) Trizol, by Thermo Fisher Scientific (2 mentions) High capacity cdna reverse transcription kit, by Thermo Fisher Scientific (2 mentions) Hiseq 3000 system, by Illumina (1 mentions) Truseq stranded mrna library preparation kit for neoprep, by Illumina (1 mentions) Paxgene blood rna kit, by Thermo Fisher Scientific (1 mentions) Ingenuity pathway analysis software, by Qiagen (1 mentions) Fragment analyzer, by Agilent Technologies (1 mentions) Taqman universal master mix 2, by Thermo Fisher Scientific (1 mentions) Quantstudio 12k flex real time pcr system, by Thermo Fisher Scientific (1 mentions) Novaseq 6000 system, by Illumina (1 mentions) Globinclear kit, by Thermo Fisher Scientific (1 mentions) Aati fragment analyzer, by Agilent Technologies (1 mentions) Agilent 2100 bioanalyzer, by Agilent Technologies (1 mentions)

5 protocols using paxgene blood rna tubes

1

RNA Sequencing of Whole Blood Samples

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We collected whole blood samples for RNA sequencing (5 mL) between 7 and 9 am after overnight fasting using PAXgene blood RNA tubes (Applied Biosystems). Tubes were shaken vigorously for at least 10 seconds after sampling and immediately stored at −80°C. We extracted total RNA using the Mag-MAX for Stabilized Blood Tubes RNA Isolation Kit (Applied Biosystems), following the manufacturer’s instructions.
We quantified RNA and assessed it for purity using NanoDrop spectrophotometry and optical density ratios of 260/280 nm and 260/230 nm. The RNA samples (1 μg per sample) were immediately sent to the Beijing Genomics Institution) for mRNA sequencing (after globin mRNA removal) on the BGIseq-500 platform. The Beijing Genomics Institution confirmed quality controls on RNA samples (RNA integrity number/RNA quality number ≥ 7.0; 28S/18S ≥ 1.0). They collected clean data of at least 4 Gb (20 M clean reads) per sample.
Pan S., Zhou Y., Yan L., Xuan F., Tong J., Li Y., Huang J., Feng W., Chen S., Cui Y., Yang F., Tan S., Wang Z., Tian B., Hong L.E., Tan Y.L, & Tian L. (2022). TGF-β1 is associated with deficits in cognition and cerebral cortical thickness in first-episode schizophrenia. Journal of Psychiatry & Neuroscience : JPN, 47(2), E86-E98.
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2

Whole Blood RNA Sequencing Workflow

Cited 1 time
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Patient’s whole blood was collected after overnight fasting using PAXgene™ blood RNA tubes (Applied Biosystems). Total RNAs were extracted using Mag-MAX™ for Stabilized Blood Tubes RNA Isolation Kit (Applied Biosystems). RNAs were quantified and immediately sent to the Beijing Genomics Institute (BGI) for mRNA sequencing by BGIseq-500. Clean data of at least 20M reads per sample were collected. Data quality control and gene expression analysis were done on the Galaxy and NetworkAnalyst platforms (29 (link)) using EdgeR. Log2 fold changes (Log2FC) with the false discovery rate (FDR) were calculated for differentially expressed genes (DEGs) (For details see Supplementary Materials).
Xuan F.L., Yan L., Li Y., Fan F., Deng H., Gou M., Chithanathan K., Heinla I., Yuan L., Seppa K., Zharkovsky A., Kalda A., Hong L.E., Hu G.F., Tan Y, & Tian L. (2022). Glial receptor PLXNB2 regulates schizophrenia-related stress perception via the amygdala. Frontiers in Immunology, 13, 1005067.
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3

Whole Blood and PBMC RNA-seq Profiling

Cited 1 time
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Total RNA was isolated from whole blood collected in PAXgene Blood RNA Tubes using PAXgene Blood RNA Kit (PreAnalytiX) per manufacturer's instructions, and PBMCs using TRIzol (Thermo Fisher Scientific). Total RNA with high quality (RIN > 8) was used for cDNA library preparation using the TruSeq Stranded mRNA Library Preparation kit for NeoPrep (Illumina). Sequencing was performed on an Illumina HiSeq 3000 System in a 1 × 50 bp single read mode. Sequenced reads were mapped against the human reference genome (GRCh37) using TopHat v2.1.1 (7 (link)). Reads mapped to hemoglobin genes were removed from further analysis. Mapped reads were quantified using HTSeq (8 (link)). All the count data were normalized using TCC (9 (link)) and differentially expressed genes were detected using edgeR (10 (link)). Pathway enrichment analysis was performed using Ingenuity Pathway Analysis (IPA) software (Qiagen), respectively. The original RNAseq data is uploaded and available online (Gene Expression Omnibus: GSE118901).
Oda H., Beck D.B., Kuehn H.S., Sampaio Moura N., Hoffmann P., Ibarra M., Stoddard J., Tsai W.L., Gutierrez-Cruz G., Gadina M., Rosenzweig S.D., Kastner D.L., Notarangelo L.D, & Aksentijevich I. (2019). Second Case of HOIP Deficiency Expands Clinical Features and Defines Inflammatory Transcriptome Regulated by LUBAC. Frontiers in Immunology, 10, 479.
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4

RNA Extraction and qRT-PCR Analysis

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RNA was extracted using MagMAX™ for Stabilized Blood Tubes RNA Isolation Kit, compatible with PAXgene™ Blood RNA Tubes (ThermoFisher). RNA concentration and purity were determined with the NanoDrop 1000 spectrophotometer (NanoDrop, Wilmington, DE), and RNA quality was assessed with the Fragment Analyzer (Agilent, Santa Clara, CA). cDNA was prepared using the High-Capacity cDNA Reverse Transcription kit (ThermoFisher Scientific) following manufacturer’s recommendations. Quantitative RT-PCR was performed on all samples in triplicate using 5 ng of cDNA per 10-ul reaction in 384-well plates with TaqMan™ assays and TaqMan™ Universal Master Mix II, no UNG on the QuantStudio 12K Flex™ Real-Time PCR System (Applied Biosystems, Foster City, CA) with the following cycling parameters: −50 °C for 2 m, 95 °C for 10 m, 40 cycles of 95 °C for 15 s and 60 °C for 1 m. Following amplification, CT values were determined using default settings of the QuantStudio 12 K Flex Software v1.2.3. TaqMan assays used for this analysis were 18S (Hs99999901_s1), HPRT (Hs02800695_m1), and TNFa (Hs00174128_m1).
Loh K.P., Wang Y., Sanapala C., Gilmore N., Netherby-Winslow C., Mendler J.H., Liesveld J., Huselton E., Williams A.M., Klepin H.D., Jensen-Battaglia M., Mustian K., Vertino P., Susiarjo M, & Janelsins M.C. (2024). Exercise and inflammatory cytokine regulation among older adults with myeloid malignancies. Experimental gerontology, 187, 112364.
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5

Comprehensive RNA Sequencing Pipeline

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RNA extraction, library preparation, and sequencing for both blood and skin samples were conducted at BGI Americas (Cambridge, Mass). Each sample had 40 million or more paired-end reads with a length of 2 × 100 bp. RNA extraction was done using the MagMAX for Stabilized Blood Tubes RNA Isolation Kit, compatible with PAXgene Blood RNA Tubes (Thermo Fisher Scientific, Waltham, Mass), according to the manufacturer's protocol with DNase digestion. The quantity and quality of extracted RNA were examined using Agilent Bioanalyzer 2100 or AATI Fragment Analyzer (Agilent Technologies, Palo Alto, Calif). The qualified total RNA from blood samples was treated for globin messenger RNA (mRNA) depletion with the GLOBINclear kit (Thermo Fisher Scientific). Purification and fragmentation of the mRNA, first-strand complementary DNA synthesis, second-strand complementary DNA synthesis, adenylation of the 3′ end, ligation of adaptors, and PCR amplification were then The library products were sequenced by the Illumina NovaSeq 6000 system.
Guttman-Yassky E., Del Duca E., Da Rosa J.C., Bar J., Ezzedine K., Ye Z., He W., Hyde C., Hassan-Zahraee M., Yamaguchi Y, & Peeva E. (2024). Improvements in immune/melanocyte biomarkers with JAK3/TEC family kinase inhibitor ritlecitinib in vitiligo. The Journal of allergy and clinical immunology, 153(1).
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