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| Status |
Public on Feb 05, 2020 |
| Title |
Modelling of pancreatic cancer biology: transcriptomic signature for 3D PDX-derived organoids and primary cell line organoid development |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
With a five-year survival rate of 9%, pancreatic ductal adenocarcinoma (PDAC) the deadliest of all cancers. The rapid mortality makes PDAC difficult to research, and inspires a resolve to create reliable, tractable cellular models for preclinical cancer research. PDAC organoids are increasing used to model PDAC as they maintain the differentiation status, molecular and genomic signatures of the original tumour. In this paper, we present novel methodologies and experimental approaches to develop PDAC organoids from PDX tumours, and the simultaneous development of matched primary cell lines. Moreover, we also identify a method of recapitulating primary cell line cultures to organoids (CLOs). We highlight the usefulness of CLOs as PDAC organoid models, as they maintain similar transcriptomic signatures as their matched patient-derived organoids and PDXs. These models provide a manageable, expandable in vitro resource for downstream applications such as high throughput screening, functional genomics, and tumour microenvironment studies.
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| Overall design |
Three biological repliates were analysed for each of the five conditions (two cell lines; two matched cell line organoid (CLO); one matched organoid) and one biological replicate for PDX sample
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| Contributor(s) |
Nelson SR, Zhang C, Roche S, O'Neill F, Swan N, Luo Y, Larkin A, Crown J, Walsh N |
| Citation(s) |
32066753 |
| Submission date |
Feb 04, 2020 |
| Last update date |
Mar 02, 2020 |
| Contact name |
Shannon Nelson |
| E-mail(s) |
shannon.nelson5@mail.dcu.ie, shannonnelson14@gmail.com, naomiwalsh@dcu.ie
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| Organization name |
DCU
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| Department |
NICB
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| Street address |
Glasnevin
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| City |
Swords |
| State/province |
Dublin |
| ZIP/Postal code |
D09 |
| Country |
Ireland |
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| Platforms (1) |
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| Samples (16)
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| Relations |
| BioProject |
PRJNA604800 |
| SRA |
SRP247192 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE144737_DESeq_counts_all_samples.xlsx |
2.2 Mb |
(ftp)(http) |
XLSX |
| GSE144737_PT291_PT127_ORG_CLO_PDX-vs-CL.xlsx |
605.3 Kb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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