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Series GSE139184 Query DataSets for GSE139184
Status Public on Jul 03, 2021
Title Transcriptomic analysis of patient-derived ex vivo models of pancreatic cancer
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary The aim of this study is to compare the transcriptomic profiles of various ex vivo models of pancreatic cancer. First, primary tumours and their corresponding xenografts in nude mice were analysed by RNA-seq. Monocultures of pancreatic cancer cells derived from the xenografts were then prepared as 2D monolayers, Matrigel-embedded organoids, spheres in suspension and 3D cultures in self-assembling peptide amphiphile (PA) hydrogels. Seven-day cultures were then analysed by RNA-seq. The results suggest that all ex vivo monocultures retain patient-specific transcriptional profiles, especially cancer stem cell signatures, while being deficient in the expression of stromal components such as the core matrisome. Correlations with the primary tumours were generally higher in PA hydrogels than organoids. Biased gene expression signatures were identified in certain models. This is the first study to explore the transcriptomic signatures of four different ex vivo models matched to their primary tumours of origin.
Overall design 29 patient-matched pancreatic adenocarcinoma (PDAC) samples were analysed: three primary PDAC tumour samples, six PDAC monocultures in PA (3 patients, duplicates), six PDAC organoid monocultures in Matrigel (3 patients, duplicates), six PDAC monocultures in 2D (3 patients, duplicates), six PDAC monocultures in suspension (3 patients, duplicates), and two primary patient-derived xenografts in grown in nude mice.
Contributor(s) Osuna de la Peña D, Loessner D
Citation(s) 34561461
Submission date Oct 21, 2019
Last update date Oct 03, 2021
Contact name David Osuna de la Peña
Organization name University College London
Department Respiratory Medicine
Street address 5 University Street
City London
ZIP/Postal code WC1E 6JF
Country United Kingdom
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (29)
GSM4133224 12556 PRI
GSM4133225 12556 PDX
GSM4133226 12560 PRI
BioProject PRJNA578718
SRA SRP226500

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Supplementary file Size Download File type/resource
GSE139184_DESeqDataSet.tsv.gz 1.4 Mb (ftp)(http) TSV
GSE139184_RAW.tar 173.9 Mb (http)(custom) TAR (of H5)
GSE139184_kallisto_tpm_allsamples.tsv.gz 16.9 Mb (ftp)(http) TSV
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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