{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Rajiv Sanwal"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15283"],"description":["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 reads"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample 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."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data 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”."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina HiSeq 2500"],"study_type":["RNA-seq of coding RNA"],"species":["Mus musculus"],"pubmed_authors":["Alexandre Hardy","Rajiv Sanwal","Elyse Latreille","Bhooma Thiruvahindrapuram","Warren Lee"],"additional_accession":[]},"is_claimable":false,"name":"RNA-Seq: Effect of Aeroplysinin-1 on gene expression in Murine RAW264.7 macrophages in basal and LPS stimulated conditions (2hours)","description":"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 reads","dates":{"release":"2025-07-14T00:00:00Z","modification":"2025-06-27T08:17:12.509Z","creation":"2025-06-27T08:17:12.509Z"},"accession":"E-MTAB-15283","cross_references":{"ENA":["ERP174132"],"Biostudies":["E-MTAB-15177"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}