Automated RNA Library Prep | Transcriptome Sequencing-Cell Samples

RNA sequencing (RNA-Seq) quantifies the transcriptome with single-nucleotide resolution, uncovering differential expression, novel transcripts, and alternative splicing. For cell-based studies, preparing transcriptome libraries across many samples is the rate-limiting step. This note presents an automated transcriptome library preparation workflow on the MGISP-960 using Yeasen’s mRNA enrichment and Ultima dual-mode RNA library chemistry.

By automating the entire workflow—from mRNA enrichment to adapter ligation—researchers can process large cohorts of cell samples with minimal hands-on time, excellent batch-to-batch reproducibility, and high library complexity, making it an ideal solution for any study that demands robust and scalable transcriptomic profiling.

Applications in Cell Transcriptomics

• Disease mechanisms & biomarkers: differential expression and fusion detection.
• Development & trait genetics: developmental timing and breeding traits.
• Drug efficacy & toxicology: dynamic response and safety profiling.
• Immunology & infection: immune-cell activation and host-pathogen dynamics.
• Comparative genomics & evolution: cross-species regulatory evolution.
• Biomarker discovery: signature genes and non-coding RNAs.

Reagent List for the Experiment

Category	Cat.No.	Product name
RNA Library Preparation	12629ES	Hieff NGS™ mRNA Isolation Master Kit V2
	12340ES	Hieff NGS™ EvoMax RNA Library Prep Kit (Strand-specific)
Magnetic Beads	12601ES	Hieff NGS™ DNA selection Beads (Superior Ampure XP alternative)
Quantification	12642ES	1× dsDNA HS Assay Kit dsDNA qubit
Adapters	12330ES	Hieff NGS™ Stubby UDI Primer Kit for Illumina, Set4（1,152 Illumina Dual-Index Unique Adapters, Plate-Format, Set 4）
User-Supplied Materials	—	Absolute Ethanol

The Automated Workflow

Figure 1. Automated transcriptome library preparation from cell samples on the MGISP-960.

Pre-Experiment Preparation

1. Equilibrate magnetic beads to room temperature before use.

2. Prepare 80% ethanol.

3. Prepare 2 herbal medicine samples and 1 rapeseed sample, each containing 400 ng of DNA. The extracted DNA shows visible pigment contamination.

Experimental Conditions and Results

Parameter	Sample 1	Sample 2	Sample 3
Sample Type	Cells	Cells	Cells
Species	Human	Rat	Mouse
Nucleic Acid Concentration (ng/μL)	187.5	120.5	466.4
Input Amount	350 ng	350 ng	350 ng
RNA Enrichment Method	mRNA Bead Capture
Fragmentation Conditions	94 °C, 7 min
Post-Ligation Purification	0.55×
Size Selection Conditions	0.60× / 0.15×
Amplification	14 cycles
Post-Amplification Purification	0.8×
Elution Volume	28 μL	28 μL	28 μL
Library Concentration (ng/μL)	37.6	38.4	49.8

Library Size Distribution

Yeasen Product Portfolio for Transcriptomic sequencing