Whole Transcriptome Sequencing – Illumina
Features
● Dual library generation to sequence the complete transcriptome: rRNA depletion library and small RNA library preparation.
● Complete bioinformatic analysis of mRNA, lncRNA, circRNA and miRNA in separated bioinformatic reports, plus a joint analysis with all RNA expression combined, including ceRNA networks analysis.
Service Advantages
● Extensive Expertise: We have processed over 2100 whole transcriptome projects, spanning diverse sample types. We bring the wealth of expertise to every project.
● Rigorous Quality Control: We implement core control points across all stages, from sample preparation to library preparation, sequencing and bioinformatics. Our 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 corresponding enrichment analyses. This comprehensive approach provides insights into the cellular and molecular processes underlying the transcriptome response, ensuring you get all the information possible about your experiment’s data.
● 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.
● Post-Sales Support: We understand how important is to be present, that’s why 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
|
Library |
Sequencing strategy |
Data recommended |
Quality Control |
|
rRNA depleted |
Illumina PE150 |
16 Gb |
Q30≥85% |
|
Size selected |
Illumina SE50 |
10-20M reads |
Sample Requirements:
Nucleotides:
|
Conc.(ng/μl) |
Amount (μg) |
Purity |
Integrity |
|
≥ 80 |
≥ 1.6 |
OD260/280=1.7-2.5 OD260/230=0.5-2.5 Limited or no protein or DNA contamination shown on gel. |
RIN≥6.0 5.0≥28S/18S≥1.0; limited or no baseline elevation |
Recommended Sample Delivery
Container: 2 ml centrifuge tube (Tin foil is not recommended)
Sample labeling: Group+replicate e.g. A1, A2, A3; B1, B2, B3.
Shipment:
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 at room temperature.
Service Work Flow
Experiment design
Sample delivery
RNA extraction
Library construction
Sequencing
Data analysis
After-sale services
Bioinformatics
On top of all the analysis on each different, the 4 types of RNA are combined into our joint analysis:
- Co-expression analysis between all the different types of RNA data
- RNA expression overview
- Diferential expression overview
- CeRNA Network
- Key genes integrated in the pathway
- Conservation analysis
- Targeting relations
RNA expression overview
Differentially Expressed genes
ceRNA analysis
Differentially 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.
