{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Bartosz Mierzejewski"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16523"],"description":["The project aimed to investigate differences in the gene expression profile of pericytes expressing the CD146 marker (CD146+ pericytes) isolated from the skeletal muscles of wild-type (WT) mice and mdx mice, which serve as a fundamental research model for Duchenne muscular dystrophy. The aim was to understand the differences between two cell types and their potential role in the disease progression. Pericytes were isolated from the skeletal muscles of WT and mdx mice and subsequently enriched for the CD146+ population using magnetic column sorting. After five days of in vitro culture, cells were harvested, and total RNA was extracted. Next-generation sequencing (NGS) was performed at the Next Generation Sequencing Core Facility, Center for New Technologies."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - CD146+ cells from both mouse strains were isolated as previously described. Briefly, isolated muscles were cut into smaller pieces, incubated in 0.2% collagenase type I in DMEM at 37 ° C for 1.5 h, followed by the additional 30 min of incubation in dispase solution in DMEM solution (2 U/ml). Cell suspension was filtered, centrifuged, and cells expressing CD146 were selected using magnetic columns (MACS; Miltenyi Biotec) and antibodies against CD146 conjugated with ferromagnetic particles, according to the manufacturers protocol. Sorted CD146+ cells were suspended in growth medium, that is, DMEM (glucose 4.5 g/l) supplemented with 15% FBS and 1% penicillin/streptomycin, seeded in culture plates and expanded under standard conditions: 37 °C, 5% CO2. Cell were cultures for 5 days, then trypsynized and subjected to RNA isolation.","Sequencing - Sequencing was performed on an Illumina NovaSeq 6000 instrument using NovaSeq 6000 S1 Reagent Kit v 1.5 (200 cycles) reagents (Illumina, Cat. No. 20028318), in a pair-end read mode of pair-end reads 2×100 cycles using the standard procedure recommended by the manufacturer with the 1 % addition of the Phix control library (Illumina, cat. no. FC-110-3001).","Nucleic Acid Extraction - Total RNA was extracted using High Pure Isolation Kit (Roche).","Library Construction - For the total RNA-seq procedure, 275 ng of RNA (RIN>9) obtained from cultured WT or mdx CD146+ cells was purified using KAPA Magnetic Beads (KAPA Biosystems, cat no. 07983298001) and then subjected to ribodepletion and library construction using the KAPA RNA HyperPrep Kit with RiboErase (KAPA Biosystems, cat. no. 08098140702) according to the manufacturer's protocol. The adapters used were KAPA_Univeral adapter and KAPA UDI primer mixes (KAPA Biosystems, cat. no. 9063781001, 9329838001). The samples were fragmented: 94 ° C 5 min, 12 enrichment cycles were performed. The resulting libraries were subjected to fragment length control using an Agilent TapeStation 4150 and a High Sensitivity D100 Reagent Kit (Agilent, cat. No.5067-5585) according to the manufacturer's protocol."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Raw sequences were trimmed according to quality using Trimmomatic (version 0.39) using default parameters, except MINLEN, which was set to 50. The cut sequences were mapped to mouse reference genome provided by ENSEMBL (version grcm38_snp_tran) using Hisat2 with default parameters. Optical duplicates were removed using the MarkDuplicates tool from GATK package (version 4.2.3.0) with default parameters except for OPTICAL_DUPLICATE_PIXEL_DISTANCE set to 12000. The mapped reads were associated with transcripts from the grcm38 database (Ensembl, version 102) using HTSeq-count (version 2.0.1) with default parameters except stranded set to “reverse”"],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of total RNA"],"species":["Mus musculus"],"pubmed_authors":["Bartosz Mierzejewski"],"additional_accession":[]},"is_claimable":false,"name":"Comparative RNA-seq analysis of CD146⁺ pericyte transcriptomes from wild-type and mdx mice","description":"The project aimed to investigate differences in the gene expression profile of pericytes expressing the CD146 marker (CD146+ pericytes) isolated from the skeletal muscles of wild-type (WT) mice and mdx mice, which serve as a fundamental research model for Duchenne muscular dystrophy. The aim was to understand the differences between two cell types and their potential role in the disease progression. Pericytes were isolated from the skeletal muscles of WT and mdx mice and subsequently enriched for the CD146+ population using magnetic column sorting. After five days of in vitro culture, cells were harvested, and total RNA was extracted. Next-generation sequencing (NGS) was performed at the Next Generation Sequencing Core Facility, Center for New Technologies.","dates":{"release":"2026-01-27T00:00:00Z","modification":"2026-01-27T02:01:58.444Z","creation":"2026-01-14T15:41:25.959Z"},"accession":"E-MTAB-16523","cross_references":{"ENA":["ERP187580"],"EFO":["EFO_0002944","EFO_0004170","EFO_0009653","EFO_0005518","EFO_0003816","EFO_0004184"]}}