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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Oct 01, 2022 |
| Title |
Transcriptome analysis revealed altered response to hypoxia, inflammation and immune regulation in Pdcd10-depleted endothelial cells |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Here we provided novel insights on the physiological functions of PDCD10 by RNA-Seq analysis, profiling Pdcd10-silenced mouse endothelial cells (ECs). We identified 53645 differentially expressed genes (DEGs) in Pdcd10-ECs compared to the respective control cell line, of which 94 reported a p-value Adjusted (pAdj) <0.05. A functional clustered dendogram generated by using ReviGO Gene ontology resource showed that the DEGs were clustered in cell proliferation, oxidative stress, vascular processes, extra-endothelial cell environment, and immune response gene ontology functions. Moreover, the major cluster of significant genes resulted to significantly enrich specific interesting signaling playing a fundamental role in inflammation and pathogen recognition, such as Hypoxia inducible factor-1 (HIF1α) and Nos2 signaling suggesting the importance of Pdcd10 in these unexplored molecular mechanisms. A validation analysis performed on wild type, Pdcd10-null and Pdcd10-null reconstituted cell lines, were found to be consistent with the sequencing data, revealing that the prioritized genes linked to the mainly meaningful pathways, have a direct functional relation with Pdcd10 expression level modulation.
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| Overall design |
RNA-Seq analysis, profiling Pdcd10-silenced mouse endothelial cells (ECs).
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| Contributor(s) |
Fusco C, Nardella G, Difilippo L, Cacchiarelli D, Petracca A, Micale L, Malinverno M, Castori M |
| Citation missing |
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| Submission date |
Oct 25, 2021 |
| Last update date |
Oct 03, 2022 |
| Contact name |
Lucio Di Filippo |
| E-mail(s) |
difilippolucio@gmail.com
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| Organization name |
ngd
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| Street address |
Via Campi Flegrei 34
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| City |
Pozzuoli |
| State/province |
Napoli |
| ZIP/Postal code |
80078 |
| Country |
Italy |
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| Platforms (1) |
| GPL21493 |
Illumina HiSeq 3000 (Mus musculus) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA774275 |
| SRA |
SRP342994 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE186523_RAW.tar |
7.4 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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