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| Status |
Public on Jun 30, 2022 |
| Title |
Bulk sequencing of MYCN-overexpressing chicken retinal cell lines |
| Organism |
Gallus gallus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Background: MYCN gene is a transcription factor whose amplification and overexpression can lead to tumorigenesis. In retina, MYCN overexpression is related to tumorigenesis of retinoblastoma, a childhood cancer.
Purpose: To find out differentially expressed genes in MYCN-overexpressing cells, which will give information of MYCN-related gene expression and possibly find out new pathways in mechanism of retinoblastoma tumorigenesis with MYCN overexpression.
Methods: MYCN-overexpressing cells were taken from MYCN electroporated E14 chicken retina and kept in culture for over 4 weeks. Unelectroporated E14 chicken retina central region was dissected as a control. Total RNA was extracted and sequenced on Illumina NovaSeq 6000. The data were used for differential expression analysis and GO/Pathway enrichment analysis.
Results: Genes related to proliferation were upregulated in MYCN-overexpressing cells, while genes related to neural differentiation were downregulated. GO/Pathway enrichment analysis showed that upregulated genes were enriched for pathways associated with cell proliferation and downregulated genes for neural differentiation.
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| Overall design |
RNA sequencing of three biological replicates of MYCN-overexpressing cell lines in long-term culture and with three replicates of E14 dissected chicken retinas as control
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| Contributor(s) |
Hallböök F, Konjusha D, Zhang H, Rafati N |
| Citation(s) |
35729105 |
| |
| Submission date |
Mar 22, 2022 |
| Last update date |
Jun 30, 2022 |
| Contact name |
Finn Hallböök |
| E-mail(s) |
finn.hallbook@igp.uu.se
|
| Organization name |
Uppsala University
|
| Department |
Dept Immunology, Genetics and Pathology
|
| Lab |
Rudbeck Laboratory
|
| Street address |
Dag Hammarskjölds v 20
|
| City |
Uppsala |
| ZIP/Postal code |
751 85 |
| Country |
Sweden |
| |
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| Platforms (1) |
| GPL26853 |
Illumina NovaSeq 6000 (Gallus gallus) |
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| Samples (6)
|
| GSM5965528 |
Control E14 chicken retina sample replicate 1 [E14.Retina.Rpt1] |
| GSM5965529 |
Control E14 chicken retina sample replicate 2 [E14.Retina.Rpt2] |
| GSM5965530 |
Control E14 chicken retina sample replicate 3 [E14.Retina.Rpt3] |
| GSM5965531 |
MYCN-overexpressing cell line in long-term culture replicate 1 [MYCN.2825] |
| GSM5965532 |
MYCN-overexpressing cell line in long-term culture replicate 2 [MYCN.2826] |
| GSM5965533 |
MYCN-overexpressing cell line in long-term culture replicate 3 [MYCN.2828] |
|
| Relations |
| BioProject |
PRJNA818671 |
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