{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Dan Brobst"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16299"],"description":["Abstract: SR12813 is an experimental cholesterol-lowering drug that reduces intracellular cholesterol through accelerated proteasomal degradation of 3-hydroxy-3-methylglutaryl-coenzyme A reductase and is also recognized as a prototypical activator of the pregnane X receptor (PXR, NR1I2). Rifampicin, a clinically used antibiotic, likewise functions as a human PXR agonist. Although PXR-mediated induction of drug metabolism genes has been extensively characterized in hepatocytes and humanized mouse liver, comparatively little is known about the transcriptional effects of these ligands in intestinal and colon cancer cells.  Here, we employed RNA sequencing in LS180 colon adenocarcinoma cells to compare transcriptional responses elicited by SR12813 and Rifampicin.  LS-180 cells were treated for 48 hours with DMSO, Rifampicin or SR12813."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - Qiagen RNAeasy as per protocol for tissue culture from 6-well plates","Sequencing - Sequencing was performed on an Illumina NextSeq 1000 system using a P2 200-cycle flow cell kit (Illumina) according to the manufacturer’s instructions.  Final pooled libraries were denatured and diluted in Illumina HT1 (Hybridization Buffer) to the recommended loading concentration for NextSeq 1000/2000 P2 200-cycle runs  The library pool was spiked with PhiX control (Illumina) at approximately 1–2% (v/v) as an internal control for run quality and error-rate estimation.  The prepared library pool was loaded onto a NextSeq 1000 P2 200-cycle flow cell and sequenced using paired-end chemistry to generate 1 × 150 bp reads with additional cycles allocated for i7 and i5 index reads according to the index design of the libraries. Cluster generation and sequencing by synthesis (SBS) were carried out automatically on the instrument using standard Illumina chemistry for the P2 200-cycle kit.","Library Construction - Total RNA (100ng) samples were converted into indexed, enriched Illumina sequencing libraries using the Illumina RNA Prep with Enrichment (L Tagmentation) kit (Illumina; catalog 20040536)","Sample Collection - Following 48hr treatment, cells were washed 2x with PBS, scraped and frozen at -80°C"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Raw Illumina BCL files were converted to FASTQ using bcl-convert v4 (Illumina). Reads were evaluated for quality using FastQC and MultiQC. No adapter trimming was performed because the sequencing run was configured with UDIs and bcl-convert handled adapter removal automatically.  Transcript-level quantification was performed using Salmon (v1.10 or similar) in quasi-mapping mode with the following settings:  --libType A  --validateMappings  --gcBias  Reference: Homo sapiens GRCh38 transcriptome (Ensembl release matching the annotation used in analysis). Salmon output (quant.sf files) was imported into R using tximport to summarize transcript-level abundances to gene-level counts.  Normalization  Gene-level count matrices produced by tximport were normalized using DESeq2 (v1.xx). Standard DESeq2 normalization steps were followed:  Size-factor estimation: DESeq2 calculated per-sample size factors using the median-ratio method.  Dispersion estimation: Gene-wise dispersion parameters were estimated followed by shrinkage using the empirical Bayesian procedure implemented in DESeq2.  Model fitting: A negative binomial generalized linear model (NB-GLM) was fit for each gene.  Transformed Data (Processed Data) Provided  The following transformed data files were generated and included in the submission:  Normalized counts: DESeq2 size-factor–normalized counts (counts(dds, normalized=TRUE))  Variance-stabilized transformation (VST): A matrix of VST-transformed gene expression values (vst(dds, blind=FALSE)), used for PCA and clustering.  Regularized log transformation (rlog): In some cases, rlog was used for visualization (rlog(dds, blind=FALSE)), but VST was the primary transformation.  Differential expression results: DESeq2 results tables for each contrast were exported, including:  log2 fold changes (shrunken using apeglm where appropriate)  Wald test p-values  Benjamini–Hochberg adjusted p-values (FDR)  Only genes passing DESeq2 internal filtering were included.  Quality Control  Downstream QC included:  PCA plots  Sample-to-sample distance matrices  MA plots  Volcano plots  Log-transformed count distributions  Outlier detection via DESeq2 Cook’s distance  No samples were excluded unless explicitly shown to be outliers by PCA and QC metrics."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NextSeq 1000"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_authors":["Dan Brobst","Brad Creamer"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq of LS180 cells treated with Rifampicin or SR12813","description":"Abstract: SR12813 is an experimental cholesterol-lowering drug that reduces intracellular cholesterol through accelerated proteasomal degradation of 3-hydroxy-3-methylglutaryl-coenzyme A reductase and is also recognized as a prototypical activator of the pregnane X receptor (PXR, NR1I2). Rifampicin, a clinically used antibiotic, likewise functions as a human PXR agonist. Although PXR-mediated induction of drug metabolism genes has been extensively characterized in hepatocytes and humanized mouse liver, comparatively little is known about the transcriptional effects of these ligands in intestinal and colon cancer cells.  Here, we employed RNA sequencing in LS180 colon adenocarcinoma cells to compare transcriptional responses elicited by SR12813 and Rifampicin.  LS-180 cells were treated for 48 hours with DMSO, Rifampicin or SR12813.","dates":{"release":"2025-12-29T00:00:00Z","modification":"2026-05-27T16:30:26.987Z","creation":"2025-11-26T23:10:30.718Z"},"accession":"E-MTAB-16299","cross_references":{"ENA":["ERP185700"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}