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| Status |
Public on Aug 10, 2021 |
| Title |
14-48h-ZH_rep1 |
| Sample type |
SRA |
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| Source name |
Retina
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
tissue: Retina
condition: hypoxia
time point: 48h
location: Zurich (400masl)
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| Treatment protocol |
For all experiments performed in Zurich (ZH), mice were placed in their homecage in isobaric hypoxia chambers and exposed to hypoxia for 6 h, 48 h, or 11 weeks. Briefly, oxygen concentration was decreased gradually by 2% every 10 min by altering the oxygen:nitrogen ratio until either 14% or 7% O2 was reached. For hypobaric experiments performed at high altitude (JFJ), mice were exposed to the environmental air pressure of approximately 64.65 kPa (slightly fluctuating depending on weather and time of the year), which decreases the ambient partial pressure of oxygen from 21.2 kPa (sea level) to 13.7 kPa
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| Extracted molecule |
total RNA |
| Extraction protocol |
Retinas were isolated through a slit in the cornea and snap-frozen in liquid nitrogen. RNA was isolated using an RNA isolation kit (Nucleo Spin RNA, Macherey-Nagel GmbH & Co.KG, Düren, Germany) with an additional, on-column DNase I treatment according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
EM4493_7
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| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRC38p5 whole genome using STAR
Genome_build: GRC38p5
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
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| Submission date |
Apr 23, 2021 |
| Last update date |
Aug 10, 2021 |
| Contact name |
Lynn Jenny Alix Ebner |
| Organization name |
Universität Zürich
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| Department |
Department of Ophthalmology
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| Lab |
Lab for Retinal Cell Biology
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| Street address |
Wagistrasse 14
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| City |
Schlieren |
| State/province |
Zürich |
| ZIP/Postal code |
8952 |
| Country |
Switzerland |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE173233 |
Acute, chronic, normobaric and hypobaric hypoxia elicit differential responses in the mouse retina on the genomic level |
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| Relations |
| BioSample |
SAMN18856622 |
| SRA |
SRX10671655 |
| 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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