{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Mengyuan Zhang"],"instrument_platform":["DNBSEQ-T7","flow cytometer (for CD146+/- cell sorting)","Agilent 2200 TapeStation system; centrifuge; Trizol reagent","VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme); manual library preparation"],"study_type":["RNA-seq of coding RNA"],"organism":["Homo sapiens"],"species":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-17450"],"description":["This study aims to characterize the transcriptomic differences between CD146-positive and CD146-negative cells isolated from human meniscus tissues. Meniscus tissue samples were collected from total knee arthroplasty (TKA) patients lacking significant joint space narrowing. CD146-positive and CD146-negative cells were isolated from each patient's meniscus tissue, yielding a total of 6 samples (3 CD146-positive and 3 CD146-negative). Total RNA was extracted using Trizol reagent, and cDNA libraries were constructed using the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina following poly(A) mRNA selection. Libraries were sequenced on the DNBSEQ-T7 platform with 150 bp paired-end reads. Raw sequencing reads were quality-filtered and aligned to the human reference genome GRCh38 (Ensemb"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - The quality and concentration of the constructed cDNA libraries were assessed using the Agilent 2200 TapeStation system. The libraries were sequenced on the DNBSEQ-T7 platform (BGI) with a 150 bp paired-end read configuration. All sequencing runs were performed according to the manufacturer's standard operating procedures.","Library Construction - cDNA libraries were constructed using the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme) following the manufacturer's instructions. Briefly, 1 μg of total RNA was used as input. Poly(A)-containing mRNA was purified using oligo(dT)-coated magnetic beads and then fragmented into 200–600 bp fragments using divalent cations at 85°C for 6 minutes. The cleaved RNA fragments were reverse-transcribed into first-strand cDNA, followed by second-strand cDNA synthesis using a dUTP mix to enable strand-specific library preparation. The cDNA fragments were then subjected to end repair, A-tailing, and ligation with indexed sequencing adapters. The adapter-ligated products were purified and treated with uracil DNA glycosylase (UDG) to remove the second-strand cDNA","Nucleic Acid Extraction - Total RNA was extracted from the isolated cell pellets using Trizol reagent (Invitrogen) according to the manufacturer's standard protocol. RNA quality and integrity were assessed using the Agilent 2200 TapeStation system. Only RNA samples with an RNA Integrity Number (RIN) greater than 7.0 were used for subsequent library construction. The extracted RNA was stored at −80°C until use.","Sample Collection - Human meniscus tissues were obtained from three non-arthritic patients undergoing surgical procedures. The tissues were processed to isolate cells, and CD146-positive and CD146-negative cell populations were separated using fluorescence-activated cell sorting (FACS) or magnetic-activated cell sorting (MACS) based on CD146 surface marker expression. The isolated cells were immediately processed for RNA extraction."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"pubmed_authors":["Mengyuan Zhang"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq of CD146-positive vs CD146-negative cells isolated from human meniscus","description":"This study aims to characterize the transcriptomic differences between CD146-positive and CD146-negative cells isolated from human meniscus tissues. Meniscus tissue samples were collected from total knee arthroplasty (TKA) patients lacking significant joint space narrowing. CD146-positive and CD146-negative cells were isolated from each patient's meniscus tissue, yielding a total of 6 samples (3 CD146-positive and 3 CD146-negative). Total RNA was extracted using Trizol reagent, and cDNA libraries were constructed using the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina following poly(A) mRNA selection. Libraries were sequenced on the DNBSEQ-T7 platform with 150 bp paired-end reads. Raw sequencing reads were quality-filtered and aligned to the human reference genome GRCh38 (Ensemb","dates":{"release":"2026-08-31T00:00:00Z","modification":"2026-08-31T01:00:47.735Z","creation":"2026-08-05T09:14:36.396Z"},"accession":"E-MTAB-17450","cross_references":{"ENA":["ERP203353"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003738","EFO_0004184"]}}