biostudies-arrayexpressBertrand-David SEGARDHomo sapiensTrimmomatic (v0.30); Hisat (v2.0.1); HTSeq (v0.6.1); DESeq (Bioconductor package)https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14788This experiment aims at comparing the transcriptomic profiles of tree subpopulations of adult human cardiac fibroblasts (aCFs) defined by their relative expression of CD90 and VCAM1. Human adult cardiac fibroblasts (aCFs) were acquired from a commercial supplier; aCF+CKs were produced by addition of TNF-α and IL-4 into the culture medium; aVCFs were isolated from aCF+CKs by MACS against CD90 and VCAM1. The RNA-seq procedure was outsourced to GENEWIZ (South Plainfield, NJ, USA), and subsequent analysis was performed in-house. Briefly, total mRNA was captured using the NEBNext Poly(A) mRNA Magnetic Isolation Module, and the library was constructed with the NEBNext Ultra RNA Library Prep Kit for Illumina. Sequencing was realized on an Illumina HiSeq 2500 System.biostudies-arrayexpressSample Collection - Human adult cardiac fibroblasts (aCFs) were acquired from a commercial supplier; aCF+CKs were produced by addition of TNF-α and IL-4 into the culture medium; aVCFs were isolated from aCF+CKs by MACS against CD90 and VCAM1.Library Construction - The library was constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs) by GENEWIZ.Nucleic Acid Extraction - Total RNA was extracted using the RNeasy Plus Mini Kit following the manufacturer’s instructions (Qiagen).Sequencing - The sequencing was realized on an Illumina HiSeq 2500 System (Illumina) by GENEWIZ.Sample Treatment - After initial expansion, aCFs were cultured with TNF-α and IL-4 in the medium. aCF-CKs were incubated with a biotin-conjugated anti-CD106 (VCAM1) or anti-CD90 (THY1) antibodies and anti-biotin microbeads for isolation of aVCFs by MACS.Growth Protocol - Human cardiac fibroblasts were cultured in HFDM-1(+) medium supplemented with 1% (v/v) Newborn Calf Serum (NBCS).OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Initial analysis was performed by GENEWIZ using the following tools: Trimmomatic (v0.30; quality control), Hisat (v2.0.1; mapping), HTSeq (v0.6.1; expression analysis), DESeq (Bioconductor package; differential expression analysis). Finally, the list of differentially expressed genes was established after correction by the Benjamini and Hochberg's approach (P-value < 0.05).Sequence Alignment - Reference genomes were downloaded from: ftp://ftp.ensembl.org/pub/release-89/gff3/homo_sapiens/Homo_sapiens.GRCh38.89.chr.gff3.gz and ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz. The alignment was done with HISAT2 (v2.0.1).UnknownTranscriptomicsGenomicsProteomicsIllumina HiSeq 2500RNA-seq of coding RNAHomo sapiensBertrand-David SEGARDTakahiro IWAMIYAfalseRNA-seq of adult cardiac fibroblasts (aCFs), aCFs treated with TNF-α and IL-4 (aCF+CKs), and aCF+CKs expressing CD90 and VCAM1 (aVCFs)This experiment aims at comparing the transcriptomic profiles of tree subpopulations of adult human cardiac fibroblasts (aCFs) defined by their relative expression of CD90 and VCAM1. Human adult cardiac fibroblasts (aCFs) were acquired from a commercial supplier; aCF+CKs were produced by addition of TNF-α and IL-4 into the culture medium; aVCFs were isolated from aCF+CKs by MACS against CD90 and VCAM1. The RNA-seq procedure was outsourced to GENEWIZ (South Plainfield, NJ, USA), and subsequent analysis was performed in-house. Briefly, total mRNA was captured using the NEBNext Poly(A) mRNA Magnetic Isolation Module, and the library was constructed with the NEBNext Ultra RNA Library Prep Kit for Illumina. Sequencing was realized on an Illumina HiSeq 2500 System.2025-10-07T00:00:00Z2025-10-07T16:28:14.415Z2025-01-28T22:07:28.183ZE-MTAB-14788ERP168710EFO_0002944EFO_0004170EFO_0003789EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_0004184EFO_0003969