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| 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
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| 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.
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| Overall design |
RNA-seq of MHCC97H, MHCCLM3 and MHCCLM6. RNC-seq of MHCCLM6.
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| |
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| Contributor(s) |
Zhibiao M |
| Citation missing |
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| |
| Submission date |
Oct 09, 2018 |
| Last update date |
Jun 03, 2019 |
| Contact name |
Zhibiao Mai |
| E-mail(s) |
[email protected]
|
| Organization name |
Jinan University
|
| Department |
Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering
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| Lab |
920
|
| Street address |
Huang-Pu Avenue West 601
|
| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510632 |
| Country |
China |
| |
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| Platforms (1) |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA495351 |
| SRA |
SRP164731 |
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