Long non-coding sequencing-Illumina
Service Advantages
Ø Service Advantages
Ø Cellular and tissue specific
Ø Specific stage expresses and presents dynamic expression change
Ø Precise patterns of time and space expression
Ø Joint analysis with mRNA data.
Ø BMKCloud-based result delivery: Customized data-mining available on platform.
Ø After-sale services valid for 3 months upon project completion
Sample Requirements and Delivery
Sample Requirements:
Nucleotides:
Tissue: Weight(dry): ≥1 g
*For tissue smaller than 5 mg, we recommend to send flash frozen(in liquid nitrogen) tissue sample.
Cell suspension: Cell count = 3×107
*We recommend to ship frozen cell lysate. In case that cell counts smaller than 5×105, flash frozen in liquid nitrogen is recommended.
Blood samples:
PA×geneBloodRNATube;
6mLTRIzol and 2mL blood(TRIzol:Blood=3:1)
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.
3.RNAstable tubes: RNA samples can be dried in RNA stabilization tube(e.g. RNAstable®) and shipped in room temperature.
Service Work Flow
Experiment design
Sample delivery
RNA extraction
Library construction
Sequencing
Data analysis
After-sale services
Bioinformatics
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1.LncRNA classification
LncRNA predicted by the four softwares above were classified into 4 categories: lincRNA, anti-sense-LncRNA, intronic-LncRNA; sense-LncRNA. LncRNA classification was shown in the histogram below.
LncRNA classification
2.Cis-targeted genes of DE-lncRNA enrichment analysis
ClusterProfiler was employed in GO enrichment analysis on cis-targeted genes of differentially expressed lncRNA (DE-lncRNA), in terms of biological processes, molecular functions and cellular components. GO enrichment analysis is a process to identify DEG-directed significantly enriched GO terms compared to whole genome. The enriched terms were presented in histogram, bubble chart, etc. as shown below.
Cis-targeted genes of DE-lncRNA enrichment analysis -Bubble chart
BMK Case
Deregulated lncRNA expression profile in the mouse lung adenocarcinomas with KRAS‐G12D mutation and P53 knockout
Published: Journal of Cellular and Molecular Medicine，2019
Sequencing strategy
Illumina
Sample collection
The NONMMUT015812-knockdown KP (shRNA-2) cells and negative control (sh-Scr) cells were obtained on day 6 of a specific viral infection.
Key results
This study investigate the aberrantly expressed lncRNAs in the mouse lung adenocarcinoma with P53 knockout and the KrasG12D mutation.
1.6424 lncRNAs were differentially expressed (≥ 2-fold change, P < 0.05).
2.Among all 210 lncRNAs(FC≥8), 11 lncRNAs’ expression was regulated by P53, 33 lncRNAs by KRAS and 13 lncRNAs by hypoxia in the primary KP cells, respectively.
3.NONMMUT015812, which was remarkably up-regulated in the mouse lung adenocarcinoma and negatively regulated by the P53 re-expression, was detected to analyse its cellular function.
4.Knockdown of NONMMUT015812 by shRNAs decreased proliferation and migration abilities of KP cells. NONMMUT015812 was a potential oncogene.
KEGG pathway analysis of the differentially expressed genes in the NONMMUT015812-knockdown KP cells |
Gene Ontology analysis of the differentially expressed genes in the NONMMUT015812-knockdown KP cells |
Reference
Deregulated lncRNA expression profile in the mouse lung adenocarcinomas with KRAS‐G12D mutation and P53 knockout[J]. Journal of Cellular and Molecular Medicine, 2019, 23(10). DOI： 10.1111/jcmm.14584
