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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jan 17, 2018 |
| Title |
Next Generation Sequencing Analysis of lung and spleen tissue transcriptomes from Wild Type KrasLA2 and miR-301a-/- Kras mice |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose: we used next generation sequencing to analyze gene expression profiles of lung and spleen tissues wild-type KrasLA2(WT-KrasLA2) and miR-301a knockout KrasLA2 (miR301aKO-KrasLA2) mice. The goals of this study are to compare the different gene expression profiles of lung tumorigenesis between WT-KrasLA2 and miR301aKO-KrasLA2 mice.
Methods: WT-KrasLA2 and miR301aKO-KrasLA2 mice were sacrificed at 9 weeks and lung and spleen tissue were obtained and total RNA was extracted. mRNA profiles were generated by deep sequencing spleen tissue in single, lung tissue from WT and miR-301a KO mice in single, lung tissue from WT-KrasLA2 and miR301aKO-KrasLA2 mice in duplicate using High-seq 2000 Illumina sequencing platform. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays
Results: After quality filtering of raw sequencing data, we obtained 47,865,482 (95%) out of 50,579,239 tags of lung, 34,855,916 (96%) out of 36,426,771 tags of spleen from WT-KrasLA2 mice, and 44,632,009 (95%) out of 46,771,631 tags of lung, 44,306,242 (94%) out of 47,032,715 tags of spleen from miR301aKO-KrasLA2 mice. We then mapped these tags to the mouse genome. We identified 1,641 DEGs (1,166 upregulated and 475 downregulated) in lung between WT-KrasLA2 and miR301aKO-KrasLA2 mice with a fold change more than 2.0 (up-regulation) or less than 0.5 (down-regulation).
Conclusions: We identified 1166 up-regulation and 475 down-regulation differentially expressed genes (DEGs) between WT-KrasLA2 and miR301aKO-KrasLA2 mice. Immune system response and cell cycle were major pathways involved in the protection role of miR-301a deletion in lung tumorigenesis. Runx3 activation is an early event identified in miR301aKO-KrasLA2 mice compared to WT-KrasLA2 mice.
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| Overall design |
Lung and spleen mRNA profiles of WT-KrasLA2 and miR301aKO-KrasLA2 mice were generated by deep sequencing, spleen tissue in single, lung tissue from WT and miR-301a KO mice in single, lung tissue from WT-KrasLA2 and miR301aKO-KrasLA2 mice in duplicate using High-seq 2000 Illumina sequencing platform.
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| Contributor(s) |
Ma X |
| Citation(s) |
31122259 |
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| Submission date |
Jan 16, 2018 |
| Last update date |
Jun 17, 2019 |
| Contact name |
Xiaodong Ma |
| E-mail(s) |
sciencema@hotmail.com
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| Phone |
5022955158
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| Organization name |
South China Normal University
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| Street address |
Rm406,Building 29, South China Normal University
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| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510631 |
| Country |
China |
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| Platforms (1) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
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| Samples (10)
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| Relations |
| BioProject |
PRJNA430230 |
| SRA |
SRP131007 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE109238_processed_data_for_all_genes.txt.gz |
77.7 Kb |
(ftp)(http) |
TXT |
| GSE109238_processed_data_for_all_genes_2.txt.gz |
565.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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