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| Status |
Public on Nov 18, 2019 |
| Title |
Gene expression data of livers from C57BL/6 treated with low dose tunicamycin |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Sustained ER stress is tightly associated with hyperglycemia and type 2 diabetes.However, the molecular mechanisms remain largely unknown.In order to identify genes that are potentially involved in ER stress-associated hyperglycemia, transcriptomics analyses were performed using RNA-sequencing,which revealed that many genes were dys-regulated in the livers of mice treated with tunicamycin.
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| Overall design |
Eight weeks old male C57BL/6 mice were purchased from the Shanghai Laboratory Animal Company (SLAC). Sustained ER stress was induced with daily intraperitoneal injections of 0.2 mg/kg tunicamycin (654380, Sigma-Aldrich) for 14 days.Then mice were sacrificed and total RNAs were isoloated from liver tissues. Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome (UCSC MM10) with hisat2 software (v2.0.4). Then, guided by the Ensembl gtf gene annotation file, cuffdiff software (part of cufflinks) was used to get the gene level FPKM as the expression profiles of mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed mRNA were identified. GO and Pathway enrichment analysis were performed based on the differentially expressed mRNAs.
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| Contributor(s) |
Liu B |
| Citation(s) |
31594848 |
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| Submission date |
Aug 05, 2019 |
| Last update date |
Nov 18, 2019 |
| Contact name |
Yan Lu |
| E-mail(s) |
lu.yan2@zs-hospital.sh.cn
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| Phone |
+86-21-64041990
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| Organization name |
Zhongshan Hospital, Fudan University
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| Department |
Department of Endocrinology and Metabolism
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| Lab |
Zhongshan
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| Street address |
180 Fenglin Road
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| City |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
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| Platforms (1) |
| GPL21103 |
Illumina HiSeq 4000 (Mus musculus) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA558676 |
| SRA |
SRP217477 |
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