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| Status |
Public on Mar 15, 2023 |
| Title |
The transcriptome profiling analysis of intestines and kidneys in conventionally raised (CV) and germ-free (GF) wild type zebrafish embryos |
| Organism |
Danio rerio |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
To investigate how the zebrafish embryos respond to the absence of the microbiota, the intestinal tissue-associated and the kidney tissue-associated gene expressions were examined at 5 dpf and 7 dpf respectively. 32,948 cDNAs of the zebrafish genome assembly were annotated after reads mapping for further analysis. For the 5 dpf intestinal tissue samples, 948 genes (4% of the total number of genes) were differentially expressed, 371 genes were up-regulated and 577 genes were down-regulated in the GF group . For the 7 dpf kidney tissue samples, 697 genes (3% of the total number of genes) were differentially expressed, 341 genes were up-regulated and 356 genes were down-regulated in the GF group. The enrichment analysis showed that the immune and cytokine related pathways were affected by the GF treatment in the wildtype embryos (both in intestines at 5 dpf and in kidneys at 7 dpf).
To investigate how the transcriptome changes in the chd8-/- zebrafish embryos, the intestinal tissue-associated and the kidney tissue-associated gene expressions were examined at 5 dpf and 7 dpf respectively.
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| Overall design |
Intestinal mRNA profiles of conventionally raised(CV) and germ-free(GF) embryos at 5 dpf,and renal (the location of their hematopoietic tissue) mRNA profiles of CV and GF embryos at 7 dpf.
Analysis of mRNA profiles of intestines at 5 dpf and renal (the location of their hematopoietic tissue) at 7 dpf in chd8-/- embryos, and comparing the data with those from the wildtype embryos.
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| Contributor(s) |
Zhong D, Jiang H, Li H |
| Citation missing |
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| Submission date |
Apr 11, 2022 |
| Last update date |
Mar 15, 2023 |
| Contact name |
Hongji Li |
| E-mail(s) |
troyli2233@sjtu.edu.cn
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| Organization name |
Shanghai Jiao Tong University
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| Department |
School of Pharmacy
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| Lab |
Lili Jing's lab
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| Street address |
Building 6, School of Pharmacy, Shanghai Jiao Tong University, No.800 Dongchuan Road, Minhang District, Shanghai
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| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200240 |
| Country |
China |
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| Platforms (1) |
| GPL24995 |
Illumina NovaSeq 6000 (Danio rerio) |
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| Samples (18)
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| Relations |
| BioProject |
PRJNA825466 |
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