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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 01, 2018 |
| Title |
176_81 |
| Sample type |
SRA |
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| Source name |
Brain
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
treatment: Sham
high fat diet: HFD
weeks: 6
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| Extracted molecule |
total RNA |
| Extraction protocol |
To obtain RNA, mice were sacrificed 3 days after stroke. Strokes are visible by eye at this time-point, and cortical tissue was dissected at 4°C that contained the stroke core and 1-2 mm of surrounding penumbral tissue, and then snap-frozen on liquid nitrogen and stored at -80°C. RNA was extracted from frozen tissue with Trizol.
RNA library preparation was performed using an Agilent Bravo automated liquid handling platform using Illumina TruSeq Stranded Total RNA HT reagents. Final libraries were assessed for quantity and quality on a Fragment Analyzer instrument (Advanced Analytical). Multiplexed paired-end libraries were sequenced on an Illumina HiSeq 4000 instrument at 300 cycles, generating on average 20-30 million reads per library sample.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Reads were trimmed of adapter sequences using trim_galore
Trimmed reads were mapped to the mm9 mouse reference genome using the STAR aligner.
Read counting was performed at the gene level using the featureCounts function in HTSeq.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited files listing raw read counts for each sample
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| Submission date |
Oct 12, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Brian D Piening |
| E-mail(s) |
bpiening@stanford.edu
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| Organization name |
Stanford
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| Department |
Genetics
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| Lab |
Snyder
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| Street address |
300 Pasteur Drive
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| City |
Palo Alto |
| State/province |
CA |
| ZIP/Postal code |
94304 |
| Country |
USA |
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| Platform ID |
GPL21103 |
| Series (1) |
| GSE104882 |
Diet-Induced Obesity Leads to Infarct Expansion, increased neuroinflammation, and Worsened Outcomes after Stroke |
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| Relations |
| BioSample |
SAMN07776836 |
| SRA |
SRX3275406 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2809423_176_81.txt.gz |
147.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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