biostudies-arrayexpressRajiv SanwalMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15283To determine the effect of Aeroplysinin-1 (Ap) on gene expression, we treated murine RAW264.7 macrophages (ATCC TIB-71) with DMSO control or Aeroplysinin-1 (1uM) for 2 hours. Unstimulated and LPS stimulated (0.1ug/mL) conditions were investigated. Three biological replicates were used per group for RNASeq analysis. Derivatives of Aeroplysinin-1 were also tested (Ap7, Ap-9) at the same concentration and time points. Aligned readsbiostudies-arrayexpressSample Collection - Lysates were prepared by washing cells twice with PBS+, lysed in recommended volume of RLT Lysis buffer from the Qiagen RNeasy RNA Isolation Kit (Cat. No. / ID: 74104) and collected by scraping with a sterile cell scraper. Lysates were vortexed for 20 seconds, centrifuged at max speed for 3 minutes at room temperature at stored at -80C for up to two weeks.Nucleic Acid Extraction - RNA was isolated using Qiagen RNeasy RNA Isolation Kit (Cat. No. / ID: 74104) by following the manufacturer's instructions.Library Construction - Library prep was performed using the NEB Ultra II Directional mRNA kit.Sequencing - Sequencing was performed with the Illumina Hiseq2500 platform with high throughput Flowcell PE2x125bp (paired end 2x125 base pair configuration), with 25-30 million reads per sample.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Two-condition differential gene expression analysis was performed with DESeq2 (https://bioconductor.org/packages/release/bioc/html/DESeq2.html and http://master.bioconductor.org/packages/release/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html) v. 1.26.0s, using R v.3.6.1. Initial minimal filtering of 10 read counts per gene for at least 3 samples was applied to the dataset. More strict filtering to increase power is automatically applied via independent filtering on the mean of normalized counts within the DESeq results() function. Note: The genes that are filtered out have padj (FDR) value of “NA”.UnknownTranscriptomicsGenomicsProteomicsIllumina HiSeq 2500RNA-seq of coding RNAMus musculusAlexandre HardyRajiv SanwalElyse LatreilleBhooma ThiruvahindrapuramWarren LeefalseRNA-Seq: Effect of Aeroplysinin-1 on gene expression in Murine RAW264.7 macrophages in basal and LPS stimulated conditions (2hours)To determine the effect of Aeroplysinin-1 (Ap) on gene expression, we treated murine RAW264.7 macrophages (ATCC TIB-71) with DMSO control or Aeroplysinin-1 (1uM) for 2 hours. Unstimulated and LPS stimulated (0.1ug/mL) conditions were investigated. Three biological replicates were used per group for RNASeq analysis. Derivatives of Aeroplysinin-1 were also tested (Ap7, Ap-9) at the same concentration and time points. Aligned reads2025-07-14T00:00:00Z2025-06-27T08:17:12.509Z2025-06-27T08:17:12.509ZE-MTAB-15283ERP174132E-MTAB-15177EFO_0002944EFO_0004170EFO_0005518EFO_0003816EFO_0003738EFO_0004184