|
| Status |
Public on Jun 01, 2019 |
| Title |
De novo assembled individual genome does not show advantage against standard reference genome: a demonstration of Chinese Han Population |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
We compared standard human reference genome GRCh38 and de novo assembled reference genome HX1 in precision medicine applications for specific ethnics. In order to quantify the HX1 misassembled genes and HX1-specific contigs, we performed RNA-seq and RNC-seq on hepatocellular carcinoma cell lines (MHCC97H, MHCCLM3 and MHCCLM6) which were derived from Chinese Han individuals. In which, RNC-seq datasets of MHCC97H and MHCCLM3 had been published. We found that a considerable fraction of HX1 misassembled genes was expressed in the Chinese Han samples. Furthermore, we found no HX1-specific contigs yielded more than 2.27 FPKM (minimun FPKM of 1 copy/cell transcript) in the Chinese Han sampels.
|
| |
|
| Overall design |
RNA-seq of MHCC97H, MHCCLM3 and MHCCLM6. RNC-seq of MHCCLM6.
|
| |
|
| Contributor(s) |
Zhibiao M |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Oct 09, 2018 |
| Last update date |
Jun 03, 2019 |
| Contact name |
Zhibiao Mai |
| E-mail(s) |
601585797@qq.com
|
| Organization name |
Jinan University
|
| Department |
Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering
|
| Lab |
920
|
| Street address |
Huang-Pu Avenue West 601
|
| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510632 |
| Country |
China |
| |
|
| Platforms (1) |
|
| Samples (4)
|
|
| Relations |
| BioProject |
PRJNA495351 |
| SRA |
SRP164731 |
Less...
More...