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| Status |
Public on Jan 04, 2024 |
| Title |
Ultra-low error synthetic long-read single-cell sequencing reveals expressions of hypermutation clusters of isoforms in human liver cancer cells |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Other
|
| Summary |
The protein diversity of mammalian cells is determined by arrays of isoforms from genes. Protein mutation is essential in species evolution and cancer development. Accurate Long-read transcriptome sequencing at single-cell level is required to decipher the spectrum of protein expressions in mammalian organisms. In this report, we developed a synthetic long-read single-cell sequencing technology based on LOOPseq technique. We applied this technology to analyze 447 transcriptomes of hepatocellular carcinoma (HCC) and benign liver from an individual. Through Uniform Manifold Approximation and Projection (UMAP) analysis, we identified a panel of mutation mRNA isoforms highly specific to HCC cells. The evolution pathways that led to the hyper-mutation clusters in single human leukocyte antigen (HLA) molecules were identified. Novel fusion transcripts were detected. The combination of gene expressions, fusion gene transcripts, and mutation gene expressions significantly improved the classification of liver cancer cells versus benign hepatocytes. In conclusion, LOOPseq single-cell technology may hold promise to provide a new level of precision analysis on the mammalian transcriptome.
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| Overall design |
HCC samples and benign liver samples were freshly dissected from a patient who underwent liver transplantation. Long-read single-cell transcriptome sequencing was performed by LoopSeq, Element Biosciences. Each library (tumor or benign) was sequenced by six runs and eventually pooled together.
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| Contributor(s) |
Liu S, Yu Y, Ren B, Yehezkel TB, Colbert C, Wang W, Ostrowska A, Soto-Gutierrez A, Luo J |
| Citation(s) |
38206124 |
| Submission date |
Jan 25, 2023 |
| Last update date |
Apr 04, 2024 |
| Contact name |
Shuchang Liu |
| E-mail(s) |
shl96@pitt.edu
|
| Organization name |
University of Pittsburgh
|
| Department |
Pathology
|
| Street address |
203 Lothrop Street
|
| City |
Pittsburgh |
| State/province |
PA |
| ZIP/Postal code |
15261 |
| Country |
USA |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (12)
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| Relations |
| BioProject |
PRJNA928094 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE223743_RAW.tar |
1.1 Gb |
(http)(custom) |
TAR (of CSV, TXT) |
| GSE223743_Supplemental_table_1.xlsx |
405.0 Kb |
(ftp)(http) |
XLSX |
| GSE223743_Supplemental_table_10.xlsx |
894.9 Kb |
(ftp)(http) |
XLSX |
| GSE223743_Supplemental_table_11.xlsx |
138.8 Kb |
(ftp)(http) |
XLSX |
| GSE223743_Supplemental_table_12.xlsx |
1.4 Mb |
(ftp)(http) |
XLSX |
| GSE223743_Supplemental_table_2.xlsx |
296.2 Kb |
(ftp)(http) |
XLSX |
| GSE223743_Supplemental_table_3.xlsx |
153.7 Kb |
(ftp)(http) |
XLSX |
| GSE223743_Supplemental_table_4.xlsx |
3.5 Mb |
(ftp)(http) |
XLSX |
| GSE223743_Supplemental_table_5.xlsx |
1.6 Mb |
(ftp)(http) |
XLSX |
| GSE223743_Supplemental_table_6.xlsx |
965.0 Kb |
(ftp)(http) |
XLSX |
| GSE223743_Supplemental_table_7.xlsx |
166.6 Kb |
(ftp)(http) |
XLSX |
| GSE223743_Supplemental_table_8.xlsx |
2.8 Mb |
(ftp)(http) |
XLSX |
| GSE223743_Supplemental_table_9.xlsx |
1.4 Mb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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