{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Etienne Kornobis"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16208"],"description":["Acute muscle injury was induced by cardiotoxin intramuscular injection in the tibialis anterior (TA) of 8-week-old Tg:Pax7nGFP mice. Mice were then housed in standard normoxic atmosphere (21%O2) or in a normobaric hypoxic chamber (10%O2), from 0 to 7 days post-injury (dpi). FACS-sorted PAX7+ (GFP+) cells were isolated from CTX-injured TAs at 7 dpi to perform a bulk RNAseq analysis."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - Total RNA was extracted from GFP+ myogenic cells isolated from injured TA using RNAqueous™-Micro Kit RNA Isolation ™ (Invitrogen™, #AM1931).","Sample Collection - Seven days after cardiotoxin-induced muscle injury, Tibialis Anterior (TA) muscles from Tg:Pax7-nGFP mice exposed to normoxic (20%) or hypoxic (10%) environment were dissected, minced and incubated with a mix of 2.4U/ml Dispase II (Roche, #04942078001) and 100μg/ml collagenase A (Roche, #11088793001) in 4.5g/L glucose 1x DMEM (GibcoTM; #11995) at 37 °C on a shaking plate for 2 h. The muscle suspension was filtrated through 100-μm and 70-μm cell strainers and then spun at 50g for 10min at 4°C to remove large tissue fragments. Then, the supernatant was collected, filtered through a 40-μm cell strainer and washed by centrifugation at 700g for 10 min at 4°C. The final pellet has been resuspended in cold 4.5g/L glucose 1xDMEM supplemented with 0.2% bovine serum albumin (BSA, Sigma-Aldrich). The muscle cell suspension was used to sort 140 000 GFP+ MuSCs by fluorescence-activated cell sorting (FACS)-sorting using the GFP reporter (n=4 per atmospheric condition).","Library Construction - Library preparation and sequencing was performed by the Biomics platform at the Institut Pasteur. RNA preparation was used to build libraries using an Illumina Stranded mRNA library Preparation Kit (Illumina, USA) following the manufacturer’s protocol. Quality control was performed on an Agilent BioAnalyzer","Sequencing - The Illumina NextSeq500 sequencer was used for the production run for 8 pooled libraries (single-end 70b reads)"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - The processed data file provided represent raw count matrix. The RNA-seq analysis was performed with Sequana 0.12.7. We used the RNA-seq pipeline 0.15.1 built on top of Snakemake 6.7.0. Briefly, reads were trimmed from adapters using Fastp 0.20.1 then mapped to the Mus musculus genome assembly GCA_000001635.9 from Ensembl using STAR 2.7.8a . FeatureCounts 2.0.1 was used to produce the count matrix, assigning reads to features using corresponding annotation v105 from Ensembl with strand-specificity information. Statistical analysis on the count matrix was performed to identify differentially regulated genes. Differential expression testing was conducted using DESeq2 library 1.30.0."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NextSeq 500"],"study_type":["RNA-seq of coding RNA"],"species":["Mus musculus"],"pubmed_authors":["Etienne Kornobis"],"additional_accession":[]},"is_claimable":false,"name":"Transcriptomic analysis of PAX7+ cells isolated from injured Tibialis Anterior muscles of mice exposed to hypoxic versus normoxic atmosphere","description":"Acute muscle injury was induced by cardiotoxin intramuscular injection in the tibialis anterior (TA) of 8-week-old Tg:Pax7nGFP mice. Mice were then housed in standard normoxic atmosphere (21%O2) or in a normobaric hypoxic chamber (10%O2), from 0 to 7 days post-injury (dpi). FACS-sorted PAX7+ (GFP+) cells were isolated from CTX-injured TAs at 7 dpi to perform a bulk RNAseq analysis.","dates":{"release":"2025-11-20T00:00:00Z","modification":"2026-06-16T13:40:19.891Z","creation":"2025-11-19T16:20:54.499Z"},"accession":"E-MTAB-16208","cross_references":{"ENA":["ERP185347"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}