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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 02, 2024 |
| Title |
Genomic characteristics of RARRES1 wild type and knockout mice lung tissues |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose: RARRES1 is proposed as tumor suppressor gene but its function is not clear yet. To elucidate RARRES1 function in carcinogenesis, we examine phenotype and genetic characteristics of the RARRES1 genetically knockout mice lung.
Methods: Genetic profiles of RARRES1 wild type and knockout mouse lung tissues of embryonic day 19.5, 10-month-old, and 18-month-old mice were analyzed by whole genome and RNA sequencing in triplicate, using Illumina Hiseq X ten. Additionally, three lung tumors originated from RARRES1 knockout mice also examine using same platform.
Results: RARRES1 knockout accelerate spontaneous lung carcinogenesis, with pluripotency of stem cells, Hippo signaling pathway, Wnt signaling pathway, and cell cycle related genes are significantly activated including Nanog, CDK1, Cyclin E. In addition, RARRES1 knockout induced lung cancer had rare oncogenic mutations, on the contrary, lung tissue progenitor cell, lung bipotent progenitor cell and AT2 type cell popularity increased.
Conclusions: RARRES1 knockout accelerate spontaneous lung carcinogenesis through organ stem cell population enhancement with various stemness related gene set activation beside rare mutational driving.
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| Overall design |
Lung whole genome and RNA profiles of triplicated embryonic day 19.5, 10-month-old, and 18-month-old wild type and RARRES1 knockout mice. Additionally, three RARRES1 knockout mice originated lung tumor were analyzed by Illumina Hiseq X ten.
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| Contributor(s) |
Yoon E, Lee SH, Yu D, Lee H, Park C, Kim K |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
May 14, 2019 |
| Last update date |
Feb 02, 2024 |
| Contact name |
Kyungtae Kim |
| E-mail(s) |
bioktkim@ncc.re.kr
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| Organization name |
National Cancer Center
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| Street address |
323 Ilsan-ro
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| City |
Goyang-si |
| State/province |
Gyeonggi-do |
| ZIP/Postal code |
10408 |
| Country |
South Korea |
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| Platforms (1) |
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| Samples (23)
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| GSM3764886 |
Rarres1-KO embryo 1 [T00_KO1] |
| GSM3764887 |
Rarres1-KO embryo 2 [T00_KO2] |
| GSM3764888 |
Rarres1-KO embryo 3 [T00_KO3] |
| GSM3764889 |
Wild-type 10-month male 1 [T10_WT1] |
| GSM3764890 |
Wild-type 10-month male 2 [T10_WT2] |
| GSM3764891 |
Wild-type 10-month male 3 [T10_WT3] |
| GSM3764892 |
Rarres1-KO 10-month male 1 [T10_KO1] |
| GSM3764893 |
Rarres1-KO 10-month male 2 [T10_KO2] |
| GSM3764894 |
Rarres1-KO 10-month male 3 [T10_KO3] |
| GSM3764895 |
Wild-type 18-month male 1 [T18_WT1] |
| GSM3764896 |
Wild-type 18-month male 2 [T18_WT2] |
| GSM3764897 |
Wild-type 18-month male 3 [T18_WT3] |
| GSM3764898 |
Rarres1-KO 18-month male (tumor) 1 [T18_KO1T] |
| GSM3764899 |
Rarres1-KO 18-month male (tumor) 3 [T18_KO3T] |
| GSM3764900 |
Rarres1-KO 18-month male (tumor) 6 [T18_KO6T] |
| GSM3764901 |
Rarres1-KO 18-month male (normal) 1 [T18_KO1N] |
| GSM3764902 |
Rarres1-KO 18-month male (normal) 2 [T18_KO2N] |
| GSM3764903 |
Rarres1-KO 18-month male (normal) 3 [T18_KO3N] |
| GSM3764904 |
Rarres1-KO 18-month male (normal) 4 [T18_KO6N] |
| GSM3764905 |
Rarres1-KO 18-month male (normal) 5 [T18_KO7N] |
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| Relations |
| BioProject |
PRJNA542797 |
| SRA |
SRP198348 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE131161_FPKM.txt.gz |
1.0 Mb |
(ftp)(http) |
TXT |
| GSE131161_readcount.txt.gz |
996.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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