biostudies-arrayexpressYang LiuHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16109Tumor tissues from 87 patients with pheochromocytoma and paraganglioma (PCPG) were collected from surgical resection specimens that had been archived as formalin-fixed paraffin-embedded (FFPE) blocks. All patients had complete clinicopathological information and follow-up records, including postoperative recurrence and distant metastasis status. For each case, one representative tumor block was selected by a pathologist, and total RNA was extracted from FFPE sections using a standard deparaffinization and RNA purification protocol. RNA libraries were prepared for bulk RNA sequencing using an FFPE-compatible workflow and sequenced on a BGISEQ platform to generate paired-end reads. This study aimed to define transcriptional subtypes of PCPG, to compare immune-microenvironment–related gene expression among subtypes, and to link expression patterns with clinical outcomes (recurrence/metastasis).biostudies-arrayexpressSequencing - Libraries were sequenced on the BGISEQ-500 (or DNBSEQ) platform to generate 150 bp paired-end reads.Nucleic Acid Extraction - Total RNA was extracted using TRIzol reagent (Thermo Fisher) or equivalent according to the manufacturer’s protocol. RNA concentration and purity were measured using NanoDrop, and RNA integrity was assessed using Agilent Bioanalyzer.Sample Collection - Tumor tissue samples were obtained during surgical resection and immediately preserved in RNAlater or snap-frozen in liquid nitrogen. Samples were stored at -80°C until RNA extraction.Library Construction - Poly(A)+ mRNA was enriched from total RNA and used to prepare cDNA libraries using a stranded mRNA library preparation protocol according to the manufacturer's instructions (BGI Genomics, Shenzhen, China).OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Raw sequencing reads were quality-controlled and trimmed to remove adaptors and low-quality bases. Clean reads were aligned to the human reference genome (GRCh38) using HISAT2 (or STAR). Gene-level read counts were quantified using featureCounts. Normalization and expression quantification were performed using DESeq2 to generate normalized counts and FPKM/TPM values. Differential expression analysis was also performed using DESeq2, following the recommended statistical workflow.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsBGISEQ-500RNA-seq of coding RNAHomo sapiensYang LiufalseTranscriptional Subtypes on Immune Microenvironment and Predicting Postoperative Recurrence and Metastasis in Pheochromocytoma and ParagangliomaTumor tissues from 87 patients with pheochromocytoma and paraganglioma (PCPG) were collected from surgical resection specimens that had been archived as formalin-fixed paraffin-embedded (FFPE) blocks. All patients had complete clinicopathological information and follow-up records, including postoperative recurrence and distant metastasis status. For each case, one representative tumor block was selected by a pathologist, and total RNA was extracted from FFPE sections using a standard deparaffinization and RNA purification protocol. RNA libraries were prepared for bulk RNA sequencing using an FFPE-compatible workflow and sequenced on a BGISEQ platform to generate paired-end reads. This study aimed to define transcriptional subtypes of PCPG, to compare immune-microenvironment–related gene expression among subtypes, and to link expression patterns with clinical outcomes (recurrence/metastasis).2025-11-17T00:00:00Z2026-05-27T16:48:22.933Z2025-11-13T10:24:08.379ZE-MTAB-16109ERP184366EFO_0002944EFO_0004170EFO_0005518EFO_0003816EFO_0003738EFO_0004184