|
| Status |
Public on Dec 11, 2018 |
| Title |
Brain vascular transcriptomes of mouse hyperglycemia mutants and controls |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Purpose:To take a comprehensive effort in characterizing the brain vasculature gene expression upon hyperglycemia.
Methods: We extracted mRNA from brain microvasculature fragments isolated from a genetic mouse model of hyperglycemia (Ins2-AKITA) and WT mice and analyzed their transcriptome with RNA sequencing The samples were sequenced on an Illumina HiSeq 2500 sequencer at the SNP&SEQ sequencing facility (Science for Life laboratory (SciLifeLab), Uppsala sequencing node). The reads were aligned to the Ensembl mouse gene assembly (NCBIM37) using Tophat2 software (version 2.0.4). The duplicated reads were removed using the picard tool (version 1.92). To identify the genes significantly enriched in the pericyte samples as compared with microvascular samples, statistical tests were performed using the Cufflinks tool (version 2.2.1)
Results: Twenty-three genes were significantly regulated in mutant when compared to WT (False Discovery Rate < 0.05)
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| |
|
| Overall design |
The microvascular RNA from two male heterozygous Ins2-AKITA mice and three littermate wild-type controls were processed and sequenced on the Illumina HiSeq 2500 platform in the sequencing facility in Uppsala University.
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| |
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| Contributor(s) |
Andaloussi Mäe M, Li T, Genové G |
| Citation(s) |
30498224 |
| |
| Submission date |
May 01, 2018 |
| Last update date |
Mar 21, 2019 |
| Contact name |
L. H. |
| Organization name |
Uppsala University
|
| Street address |
Dag Hammarskjölds Väg 20
|
| City |
Uppsala |
| ZIP/Postal code |
751 85 |
| Country |
Sweden |
| |
|
| Platforms (1) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
|
| Samples (5)
|
| GSM3123550 |
Isolated brain microvascular fragments (wildtype control 1) |
| GSM3123551 |
Isolated brain microvascular fragments (wildtype control 2) |
| GSM3123552 |
Isolated brain microvascular fragments (wildtype control 3) |
| GSM3123553 |
Isolated brain microvascular fragments (heterozygous Ins2-AKITA mutant 1) |
| GSM3123554 |
Isolated brain microvascular fragments (heterozygous Ins2-AKITA mutant 2) |
|
| Relations |
| BioProject |
PRJNA454465 |
| SRA |
SRP144201 |
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