RNA-Seq (Transcriptome) of xen

Introduction

Human tumor xenografts constitute the major efficacy and tumor biology models for cancer drug discovery. Tumors can be maintained by serial xenografting in athymic (nude) or severe combined immunodeficient (SCID) mice (Teicher 2009). Sequences that are very similar between the two genomes may be impossible to deconvolute, however. The similar sequences between human and mouse covers nearly 13% of the human genome. A variation in a human sequence can masquerade as a mouse sequence if the novel human variation now matches a mouse sequence perfectly. Simulations suggest that the confusion cannot be detectable in a mixture, regardless of the level of sequencing coverage achieved (Ming-Tseh Lin and Tseng 2010). Thus, the pivotal duty is to exclude the possibility of mouse genomic DNA contamination.
RNA‐Seq (Transcriptome) is a powerful tool to measure mRNA expression and detect SNP, RNA editing, alternative splicing and gene fusions, which may contribute to the cancer development.
In BGI, there are two strategies for the xenograft tumor transcriptome sequencing, which both take into account the non-malignant contamination in xenograft largely from murine cells.

Sample requirement:

RNA-Seq (xenograft samples):
Sample condition: Integrated total RNA samples that are treated by DNase; Avoid protein contamination during RNA isolation; Sample quantity: total RNA ≥ 5 μg; Sample concentration: ≥ 80 ng/μl; Sample purity: OD260/280 = 1.8~2.2; OD260/230 ≥ 2.0; 28S:18S > 1.0 and RIN ≥ 7.0
WGRS (host mouse samples):
Sample condition: DNA samples without degradation and RNA contamination; Sample quantity demanded: ≥ 6 μg; Sample concentration: 50-200 ng/μl; Sample purity: OD260/280 =1.8~2.0.

Data Delivery

All of the data shall be delivered via either BGI FTP site or hard drive.