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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Oct 29, 2019 |
| Title |
agonist 5830 |
| Sample type |
SRA |
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| Source name |
Aorta
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| Organism |
Mus musculus |
| Characteristics |
strain: apoe-/-
tissue: thoracic aorta
age: 18 weeks
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| Treatment protocol |
Mice were treated with α7nAChR agonist AZ6983 (50 µmol kg-1 per day) or vehicel for 8 weeks using osmotic minipumps
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| Extracted molecule |
total RNA |
| Extraction protocol |
Thoracic aorta was dissected, snap frozen in liquid nitrogen and RNA was extracted by using the RNAeasy® Fibrous Tissue Mini Kit (Qiagen GmbH, Hilden, Germany) according to the manufacturer’s protocol.
TrueSeq stranded Total RNA Sample preparation with RiboZero Gold, following protocol 15031048 Rev E
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
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| Data processing |
Base-calling, CASAVA 1.8.2
Data trimming, prinseq 0.20.3, parameters: -min_qual_mean 20 -ns_max_ p 10 -trim_qual_right 3 -min_len 30
Alignment, STAR 2.5.2b
Gene-counts, htseq 0.6.1p1
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited raw gene counts containing all samples
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| Submission date |
May 14, 2019 |
| Last update date |
Oct 29, 2019 |
| Contact name |
Maria E Johansson |
| E-mail(s) |
maria.e.johansson@neuro.gu.se
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| Organization name |
University of Gothenburg
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| Department |
Physiology
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| Street address |
Medicinaregatan 11
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| City |
Gothenburg |
| ZIP/Postal code |
405 30 |
| Country |
Sweden |
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| Platform ID |
GPL21626 |
| Series (1) |
| GSE131162 |
RNA sequencing data describing transcriptional changes in aorta of ApoE-/- mice after alpha 7 nicotinic acetylcholine receptor (α7nAChR) stimulation. |
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| Relations |
| BioSample |
SAMN11638378 |
| SRA |
SRX5827908 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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