{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["guosheng Wang"],"organism":["Rattus norvegicus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16153"],"description":["We constructed a rat model of femoral osteomyelitis by injecting a mixture of Staphylococcus aureus suspension and LPS.  Subsequently, we performed RNA-seq to compare the osteomyelitic femur with the normal femur group."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - In this study, five femoral tissue samples were collected from the chronic osteomyelitis model group and the control group each, resulting in a total of ten samples.","Library Construction - For each sample, 500 ng of total RNA was used for cDNA synthesis via a strand-switching reverse transcription approach. The resulting cDNA was then amplified by PCR, followed by barcoding with the Native Barcode kit (SQK-NBD114.96) and purification using Ampure XP Beads. Finally, 300 fmol of the resulting library was loaded onto a PromethION flow cell (vR10.4.4) for sequencing.","Nucleic Acid Extraction - Total RNA extraction using Total RNA extraction Kit (DP431, TIANGEN, China). The quality and quantity of the purified RNA were determined by measuring the absorbance at 260nm/280nm(A260/A280) using Ultrafine spectrophotometer (N50 touch, IMPLEN, Germany). The integrity of RNA was further verified by 1.0% agarose gel electrophoresis","Sequencing - We used the Oxford nanopore technology (ONT) to sequence from AS and HC"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - To evaluate the accuracy of abundance estimation with transcript and gene resolution, we used the quasi-mapping mode of Salmon(v1.7.0) [17] to estimate the TPM for each transcript and gene in each of the sample data."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["PromethION"],"study_type":["RNA-seq of coding RNA"],"species":["Rattus norvegicus"],"pubmed_authors":["guosheng Wang"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq of rat tissues with chronic osteomyelitis","description":"We constructed a rat model of femoral osteomyelitis by injecting a mixture of Staphylococcus aureus suspension and LPS.  Subsequently, we performed RNA-seq to compare the osteomyelitic femur with the normal femur group.","dates":{"release":"2025-12-10T00:00:00Z","modification":"2026-05-30T17:25:19.459Z","creation":"2025-11-11T14:59:52.041Z"},"accession":"E-MTAB-16153","cross_references":{"ENA":["ERP184213"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}