BMKCloud Log in


Whole transcriptome sequencing – Illumina

Whole transcriptome sequencing offers a comprehensive approach to profiling diverse RNA molecules, encompassing both coding (mRNA) and non-coding RNAs (lncRNA, circRNA, and miRNA). This technique captures the full transcriptome of specific cells at a given moment, allowing for a holistic understanding of cellular processes. Also known as “total RNA sequencing,” it aims to unveil intricate regulatory networks at the transcriptome level, enabling in-depth analysis such as competing endogenous RNA (ceRNA) and joint RNA analysis. This marks the initial step towards functional characterization, particularly in unraveling the regulatory networks involving circRNA-miRNA-mRNA-based ceRNA interactions.

Service Details


Demo Results

Featured Publications


●  Dual library to sequence the complete transcriptome: rRNA depletion followed by PE150 library preparation and size selection followed by SE50 library preparation

●  Complete bioinformatics analysis of mRNA, lncRNA, circRNA and miRNA in separate bioinformatics reports

● Joint analysis of all RNA expression in combined report, including ceRNA networks analysis.

Service Advantages

● In-depth analysis of regulatory networks: ceRNA network analysis is enabled by the joint sequencing of mRNA, lncRNA, circRNA and miRNA and by an exhaustive bioinformatic workflow.

● Comprehensive Annotation: we use multiple databases to functionally annotate the Differentially Expressed Genes (DEGs) and perform the corresponding enrichment analysis, providing insights on the cellular and molecular processes underlying the transcriptome response.

● Extensive Expertise: with a track record of successfully closing over 2000 whole transcriptome projects in various research domain, our team brings a wealth of experience to every project.

● Rigorous Quality Control: we implement core control points across all stages, from sample and library preparation to sequencing and bioinformatics. This meticulous monitoring ensures the delivery of consistently high-quality results.

● Comprehensive Annotation: we use multiple databases to functionally annotate the Differentially Expressed Genes (DEGs) and perform the corresponding enrichment analysis, providing insights on the cellular and molecular processes underlying the transcriptome response.

● Post-Sales Support: Our commitment extends beyond project completion with a 3-month after-sale service period. During this time, we offer project follow-up, troubleshooting assistance, and Q&A sessions to address any queries related to the results

Sample Requirements and Delivery


Sequencing strategy

Data recommended

Quality Control

rRNA depleted

Illumina PE150

16 Gb


Size selected

Illumina SE50

10-20M reads


Sample Requirements:



Amount (μg)



≥ 100

≥ 1



Limited or no protein or DNA contamination shown on gel.

Plants: RIN≥6.5

Animal: RIN≥7.0


limited or no baseline elevation

Recommended Sample Delivery

2 ml centrifuge tube (Tin foil is not recommended)
Sample labeling: Group+replicate e.g. A1, A2, A3; B1, B2, B3... ...

1.Dry-ice: Samples need to be packed in bags and buried in dry-ice.
2.RNAstable tubes: RNA samples can be dried in RNA stabilization tube(e.g. RNAstable®) and shipped in room temperature.

Service Work Flow

Sample QC

Experiment design

sample delivery

Sample delivery

Pilot experiment

RNA extraction

Library Preparation

Library construction



Data analysis

Data analysis

After sale Services

After-sale services

  • Previous:
  • Next:

  • Bioinformatics


    RNA expression overview


    Differentially Expressed genes




    ceRNA analysis

     图片43Differentially expressed miRNAs and related RNAs


     Explore the research advancements facilitated by BMKGene’ whole transcriptome sequencing services through a curated collection of publications.


    Dai, Y. et al. (2022) ‘Comprehensive expression profiles of mRNAs, lncRNAs and miRNAs in Kashin-Beck disease identified by RNA-sequencing’, Molecular Omics, 18(2), pp. 154–166. doi: 10.1039/D1MO00370D.

    Liu, N. nan et al. (2022) ‘Full length transcriptomes analysis of cold-resistance of Apis cerana in Changbai Mountain during overwintering period.’, Gene, 830, pp. 146503–146503. doi: 10.1016/J.GENE.2022.146503.

    Wang, X. J. et al. (2022) ‘Multi-Omics Integration-Based Prioritisation of Competing Endogenous RNA Regulation Networks in Small Cell Lung Cancer: Molecular Characteristics and Drug Candidates’, Frontiers in Oncology, 12, p. 904865. doi: 10.3389/FONC.2022.904865/BIBTEX.

    Xu, P. et al. (2022) ‘Integrated analysis of the lncRNA/circRNA-miRNA-mRNA expression profiles reveals novel insights into potential mechanisms in response to root-knot nematodes in peanut’, BMC Genomics, 23(1), pp. 1–12. doi: 10.1186/S12864-022-08470-3/FIGURES/7.

    Yan, Z. et al. (2022) ‘Whole-transcriptome RNA sequencing highlights the molecular mechanisms associated with the maintenance of postharvest quality in broccoli by red LED irradiation’, Postharvest Biology and Technology, 188, p. 111878. doi: 10.1016/J.POSTHARVBIO.2022.111878.

  • get a quote

    Write your message here and send it to us

    Send your message to us: