{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Eugenia Ong"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14343"],"description":["RNA was extracted from whole blood of subjects collected in Tempus tubes. We performed gene expression analysis of dengue seropositive versus dengue seronegative subjects from Singapore."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - Blood was collected in Tempus tubes from subjects, and Tempus tubes were stored at -80deg until RNA extraction. We performed gene expression analysis of dengue seropositive versus dengue seronegative subjects.","Nucleic Acid Extraction - RNA extraction from whole blood was performed using the Tempus Spin RNA Isolation kit (Thermo Scientific). RNA was eluted in 90ul of RNase-free water.","Library Construction - 1 μg total RNA was used for following library preparation. The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was treated to repair both ends and add a dA-tailing in one reaction, 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 an Illumina Novaseq instrument for sequencing using a 2x150 paired-end (PE) configuration according to manufacturer’s instructions."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data 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 16 samples with at least 10 reads were included for analysis. The number of samples were determined by the minimum number of samples present in each comparison group. 16,374 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. Log2 fold-changes and p-values were obtained from DESeq2’s results function.","Sequence Alignment - Short-read alignment was performed using Hisat2 (v2.0.1) with default parameters to the reference genome Emsembl GRCh38.p13."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_authors":["Eugenia Ong"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq for dengue seronegative and dengue seropositive individuals from Singapore","description":"RNA was extracted from whole blood of subjects collected in Tempus tubes. We performed gene expression analysis of dengue seropositive versus dengue seronegative subjects from Singapore.","dates":{"release":"2025-09-08T00:00:00Z","modification":"2025-09-09T00:01:42.806Z","creation":"2024-08-07T13:51:20.508Z"},"accession":"E-MTAB-14343","cross_references":{"ENA":["ERP163070"],"EFO":["EFO_0002944","EFO_0004170","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}