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| Status |
Public on Jul 14, 2023 |
| Title |
Long-read transcriptome profiling of human lung cancer cell lines |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose: The aim of this study is to compare the transcriptome profiles using a mixture design that allows the relative changes of the majority of the genes profiled to be estimated. Methods - Cell Culture: Lung adenocarcinoma cell lines NCI-H1975 and HCC827 were grown in Roswell Park Memorial Institute (RPMI) 1640 medium with 10% fetal calf serum and 1% penicillin-streptomycin. Methods - RNA preparation: mRNA was extracted using a Qiagen RNA miniprep kit and purified using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (E7490). Purified mRNA spiked with sequins was used for the cRNA-PCR Barcoding (SQK-PCS109 with SQK-PBK004) kit (ONT). Completed libraries were sequenced on PromethION (ONT). Reads were mapped to known genomic features of the GrCh38 reference transcriptome and RNA sequin transcriptome combined sequences at the transcript-level and single reads were then summarized into transcript-level counts using salmon software (Patro et al. 2017).
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| Overall design |
Total RNA was extracted from lung adenocarcinoma cell lines NCI-H1975 and HCC827. Total RNA transcriptome from these samples was profiled by RNA-seq (Oxford Nanopore Technologies PromethION).
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| Contributor(s) |
Dong X, Jabbari JS, Gouil Q, Du MM, Ritchie ME |
| Citation(s) |
37783886 |
| |
| Submission date |
Mar 09, 2023 |
| Last update date |
Oct 15, 2023 |
| Contact name |
Matthew Ritchie |
| E-mail(s) |
mritchie@wehi.edu.au
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| Organization name |
The Walter and Eliza Hall Institute of Medical Research
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| Street address |
1G Royal Parade
|
| City |
Parkville |
| State/province |
Victoria |
| ZIP/Postal code |
3052 |
| Country |
Australia |
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| Platforms (1) |
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| Samples (5)
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| GSM7089881 |
NCI-H1975 + sequins mixA mixed with HCC827 + sequins mixB in ratio 100:0 |
| GSM7089882 |
NCI-H1975 + sequins mixA mixed with HCC827 + sequins mixB in ratio 75:25 |
| GSM7089883 |
NCI-H1975 + sequins mixA mixed with HCC827 + sequins mixB in ratio 50:50 |
| GSM7089884 |
NCI-H1975 + sequins mixA mixed with HCC827 + sequins mixB in ratio 25:75 |
| GSM7089885 |
NCI-H1975 + sequins mixA mixed with HCC827 + sequins mixB in ratio 0:100 |
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| Relations |
| BioProject |
PRJNA942630 |
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