biostudies-arrayexpressJustin OoiHomo sapiensDESeq2https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14708This study investigates the post-vaccination gene expression associated with protective T cell levels and why it takes two doses to boost an anamnestic response in older adults using the AS01b-adjuvanted recombinant zoster vaccine (RZV, ShingrixTM). The experiment is the transcriptional profiling of peripheral blood mononuclear cells (PBMCs) from 15 healthy adults with age 50 – 65 years old collected at day 0, day 1, day 4 and day 14 post-dose 1 and day 60, day 61, day 64 and day 74 post-dose 2.biostudies-arrayexpressSample Collection - Blood was drawn from subjects into Tempus tubes and RNA extraction performed.Nucleic Acid Extraction - RNA isolation from whole blood was performed using the Tempus Spin RNA Isolation Kit, eluted in 90uL elution buffer and stored at -80C.Library Construction - 1 μg total RNA was used for library preparation by Azenta Life Sciences. Poly(A) mRNA isolation was performed using Oligo(dT) beads and mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using random primers followed by synthesis of first strand and the second-strand cDNA. Purified cDNA was then treated to repair both ends and dA-tailing added, followed by a T-A ligation to add adaptors to both ends. Size selection of adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.Sequencing - Libraries with different indexes were multiplexed and loaded on the Illumina Novaseq instrument for sequencing using a 2x150bp paired-end configuration according to manufacturer’s instructions.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Raw counts from RNA sequencing data were normalized through the DESeq2 (v1.42.0) R package. The raw counts were averaged out for duplicate gene reads and genes present in a minimum of 15 samples with at least 10 reads. The number of samples were determined by the minimum number of samples present in each comparison group. The filtering yielded 17,405 genes. The filtered genes were then normalized by the DESeq function in DESeq2, which estimates each sample’s size factors, gene-wise dispersions, fits the values to a negative binomial distribution model and conducts a Wald statistical test. Normalized counts were obtained from DESeq2’s was then used to calculate the log2counts and log2 fold-changes.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina HiSeq 2000RNA-seq of coding RNAHomo sapiensAS01-adjuvanted vaccine alters baseline correlates of T cell response to varicella zoster virus in older adultsKuan Rong ChanCandice ChanJustin OoiCandice C.Y. Chan, Justin S.G. Ooi, Clara W.T. Koh, Eugenia Z. Ong, Christine Y.L. Tham, Jia Xin Yee, Valerie S.Y. Chew, Yin Bun Cheung, Eng Eong Ooi, Jenny G. Low, Kuan Rong ChanfalseGene expression changes in older adults post-Shingrix vaccinationThis study investigates the post-vaccination gene expression associated with protective T cell levels and why it takes two doses to boost an anamnestic response in older adults using the AS01b-adjuvanted recombinant zoster vaccine (RZV, ShingrixTM). The experiment is the transcriptional profiling of peripheral blood mononuclear cells (PBMCs) from 15 healthy adults with age 50 – 65 years old collected at day 0, day 1, day 4 and day 14 post-dose 1 and day 60, day 61, day 64 and day 74 post-dose 2.2025-07-07T00:00:00Z2025-07-07T11:01:18.91Z2024-12-17T14:29:42.631ZE-MTAB-14708ERP167249EFO_0002944EFO_0004170EFO_0005518EFO_0003816EFO_0003738EFO_000418410.1016/j.vaccine.2025.127396