biostudies-arrayexpressJustin OoiHomo sapiensDESeq2https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15195This study investigates the post-vaccination gene expression associated with T cell response and why humoral immunity does not inform cellular responses post-vaccination. The experiment is the transcriptional profiling of peripheral blood mononuclear cells (PBMCs) from 21/27 subjects collected at day 0 and day 1 post-vaccination (Dose 1).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 sapiensNeutralizing antibody titers do not predict T cell response to live-attenuated orthoflaviviral vaccination in humansJustin S.G. Ooi, Noor Zayanah Hamis, Hwee Cheng Tan, Jia Xin Yee, Valerie S.Y. Chew, Joey Ming Er Lim, Eugenia Z. Ong, Kuan Rong Chan, Laura Rivino, Jenny G. Low, Eng Eong Ooi, Shirin KalimuddinKuan Rong ChanJustin OoifalseEarly gene expression after COVID-19 mRNA (BNT162b2) vaccination that is associated with spike-specific T cell responsesThis study investigates the post-vaccination gene expression associated with T cell response and why humoral immunity does not inform cellular responses post-vaccination. The experiment is the transcriptional profiling of peripheral blood mononuclear cells (PBMCs) from 21/27 subjects collected at day 0 and day 1 post-vaccination (Dose 1).2026-04-21T00:00:00Z2026-04-21T14:59:26.261Z2025-06-09T14:37:52.416ZE-MTAB-1519541880822ERP173286EFO_0002944EFO_0004170EFO_0005518EFO_0003816EFO_0003738EFO_000418410.1016/j.vaccine.2026.128510