---
title: "Eukaryotic RNA-seq"
lang: en
url: https://www.gereallife.com/en/services/rna-seq.html
canonical: https://www.gereallife.com/en/services/rna-seq.html
entity: Shanghai Gereallife Biotech Co., Ltd
updated: 2026-11-02
---
TRANSCRIPTOMICS 
 

# Eukaryotic RNA-seq

 

Eukaryotic Transcriptome Sequencing — Expression & Differential Analysis

 

Eukaryotic RNA-seq provides a panoramic view of mRNA expression: total RNA is enriched for mRNA with Oligo(dT) magnetic beads, library-prepped and sequenced; after QC, reads are aligned to the reference genome with STAR for gene/transcript-level quantification, followed by differential expression, GO / KEGG enrichment and GSEA analyses.

 
 
 Oligo(dT) mRNA Enrichment & Library Prep mRNA ENRICHMENT STAR Reference Genome Alignment REFERENCE ALIGNMENT 8 Analysis Modules ANALYSIS MODULES 

## Technical Specifications

 TECHNICAL SPECIFICATIONS 

| Item | Details |
| --- | --- |
| Library Prep | Oligo(dT) bead-based mRNA enrichment |
| Read Alignment | STAR aligns cleaned reads to the reference genome; sequencing and library quality assessed by mapping rate, insert size and coverage uniformity |
| Quantification | Gene/transcript quantification against the annotation, outputting Count, FPKM, TPM and log2TPM |
| DE Thresholds | Read-count normalization (depth correction) → statistical modeling for P values → BH adjustment (padj); default |log2(FoldChange)| > 1 and padj < 0.05 |
| Standard Delivery | Raw data + analysis report |

 
 

## Analysis Workflow

 ANALYSIS WORKFLOW 1 Data QC Adapter trimming · rRNA assessment 2 Read Alignment STAR · reference genome 3 Quantification Count / FPKM / TPM 4 Expression QC Correlation · PCA 5 Differential Analysis Volcano · clustering 6 GO Enrichment BP / CC / MF 7 KEGG Enrichment Pathways · bubble plots 8 GSEA GO / KEGG gene sets 
 

## Bioinformatics Analyses

 BIOINFORMATIC MODULES 

| Module | Core Methods & Metrics | Key Outputs |
| --- | --- | --- |
| Sequencing Statistics | Base-quality and content distributions of raw fastq (R1/R2); 3′/5′ adapter trimming; filtering reads with mean quality < 20 or length < 50 bp and reads containing N; rRNA contamination rate assessment | Raw and cleaned data statistics tables, base-quality and content distribution plots |
| Alignment QC | STAR aligns cleaned reads to the reference genome; sequencing and library quality assessed at checkpoints including mapping rate, insert size and coverage uniformity | Mapping-rate statistics tables, per-sample alignment detail plots |
| mRNA Quantification | Gene/transcript quantification against the annotation with Count, FPKM, TPM and log2TPM outputs; Top-10 highly expressed transcripts summarized | Expression matrices, Top-10 expression tables |
| Expression Distribution & QC | Expression density distributions; per-sample violin/box plots; inter-sample Pearson correlation heatmaps (ideal within-group R² > 0.9) and PCA | Density plots, violin/box plots, correlation heatmaps, PCA plots |
| Differential Analysis | Read-count normalization (depth correction) → statistical modeling for P values → BH multiple-testing adjustment (padj); default |log2(FoldChange)| > 1 and padj < 0.05 | Differential analysis result tables, volcano plots |
| DE Patterns | Expression-pattern clustering of differential genes; shared and unique DEG statistics across multiple comparisons | Pattern-clustering heatmaps, shared-DEG diagrams |
| GO Functional Enrichment | GO enrichment of DEGs (BP / CC / MF), reporting GeneRatio / BgRatio, enrichment factor and adjusted p-values | GO enrichment bubble and bar plots |
| KEGG & GSEA | KEGG pathway enrichment of DEGs; GSEA based on GO and KEGG gene sets, reporting ES, NES and adjusted p-values | KEGG enrichment plots, GSEA enrichment plots and dot plots |

 
 

## Example Results

 SELECTED FIGURES FROM ACTUAL REPORTS Gene Expression Density log2(TPM) density curves per sample, assessing consistency of expression distributions. Expression Violin / Box Plots Distribution and probability density of gene-expression values per sample; boxes show medians and quartiles. Inter-Sample Correlation Heatmap Pairwise Pearson correlations and hierarchical clustering of samples, assessing biological-replicate consistency. Inter-Sample PCA Sample distribution after dimensionality reduction, showing intergroup separation and within-group clustering. Differential Expression Volcano Plot Dual thresholds of log2(FoldChange) and −log10(P) mark up/down-regulated genes, with key genes labeled. DEG Expression-Pattern Clustering Expression patterns of DEGs across samples (log10 TPM), with two-way clustering of genes and samples. GO Functional Enrichment (Excerpt) Enrichment results and significance of GO terms (BP / CC / MF) for DEGs; top terms shown. GO-based GSEA Enrichment Plot Enrichment-score curves with ranked-gene positions, annotated with NES and adjusted p-values. KEGG-based GSEA Dot Plot Gene ratios and significance of KEGG pathway enrichment; dot size indicates enriched gene counts. 
 

## FAQ

 FAQ 
 How long does a Eukaryotic RNA-seq project take? From sample QC approval, standard timelines are 3-6 weeks (library prep, sequencing and bioinformatics included); large cohorts or deep custom analyses follow the confirmed study plan. What if my samples fail QC? Failed QC is reported immediately with reasons, and we discuss resampling or plan adjustments with you — sequencing never proceeds without qualification. What bioinformatics is included? Can I add custom analyses? Standard delivery covers QC, mapping/assembly, quantification, differential and functional enrichment analyses. Custom deep-dive and multi-omics integrative analyses are supported on request. What samples do you need for Eukaryotic RNA-seq? Total RNA ≥1 μg with RIN ≥7 (snap-frozen, dry ice); microbial and faecal samples ≥200 mg (sterile, −80 °C); whole blood for WGS ≥500 μL (EDTA only, never heparin). RNA integrity matters more than concentration. See Technical Resources → Sample Guide . 
 
 

## Related Services

 RELATED SERVICES 
 

### Amplicon Sequencing

Amplicon Sequencing

 

### Metagenomics

Metagenomics

 

### Whole Genome Sequencing

Whole Genome Sequencing

 
 
 

Delivery timing: sample shipping, customs declaration and similar steps may extend turnaround; actual project timelines prevail.

 
 
 
 

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