 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Feb 26, 2022 |
| Title |
To detect full-length genome of intron 19 of ARFGEF1 [intron19arfgef1] |
| Organism |
Homo sapiens |
| Experiment type |
Other
|
| Summary |
Analysis of high-throughput transcriptome sequencing (RNA-seq) data often observed numerous 'non-co-linear' (NCL) transcripts, which may originate from genetic rearrangements (gene fusion) indicated the importance of fusion events and circRNAs in carcinogenesis; however, the role of ts-RNAs remains largely uninvestigated. Here we developed a hybrid sequencing pipeline ("NCLscan-hybrid"), which integrated different types of short (Illumina-based) and extra-long (PacBio-based) RNA-seq data to eliminate potential false positives from experimental artifacts, fusion events, and circRNAs. We applied NCLscan-hybrid to investigate of ts-RNAs in human breast cancer, the most malignant tumors diagnosed in women worldwide. Through multiple experimental validation steps, we confirmed that the intragenic ts-RNA, ts-ARFGEF1, was highly expressed in breast cancer cells but absent in normal breast cells. Furthermore, we experimentally validated that ts-ARGEF1 can contribute to cell proliferation and apoptosis. Analysis of xenograft in nude mice showed that disruption of ts-ARFGEF1 expression can significantly attenuate tumor growth. Microarray analysis revealed that ts-ARFGEF1 knockdown could trigger PERK/ATF4/CHOP signaling pathway, implying the function of ts-ARFGEF1 in ER homeostasis. Taken together, our findings provide an in-depth view of the true complexity of intragenic NCL events and, for the first time, show further insight into the potential roles of intragenic ts-RNAs in tumor cell development.
|
| |
|
| Overall design |
We designed primer to amplify the region of intron 19 of ARFGEF1 and then the purified PCR products were subjected to nanopore sequencing
|
| |
|
| Contributor(s) |
Chuang T |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
Feb 23, 2022 |
| Last update date |
Feb 27, 2022 |
| Contact name |
Trees-Juen Chuang |
| E-mail(s) |
[email protected]
|
| Organization name |
Academic Sinica
|
| Department |
Genomics Research Center
|
| Street address |
128 Academia Road, Section 2, Nankang, Taipei, 115, Taiwan
|
| City |
Taipei |
| ZIP/Postal code |
11529 |
| Country |
Taiwan |
| |
|
| Platforms (1) |
|
| Samples (1) |
|
| Relations |
| BioProject |
PRJNA809824 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE197337_RAW.tar |
10.0 Kb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
