|
| Status |
Public on Jul 13, 2020 |
| Title |
male hypoxia cervical cord replicate 5 [MHV_S15] |
| Sample type |
SRA |
| |
|
| Source name |
male hypoxia cervical cord
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: sprague dawley
Sex: male
air treatment: hypoxia
tissue: C3-C6 spinal cord
cell type: C3-C6 spinal cord microglia
|
| Treatment protocol |
Intermittent exposures consisted of 8 hours of exposure per day, with 15 cycles per hour. Normoxia exposures consisted of room air (21%/21% O2), while hypoxia exposures consisted of alternating 10.5%/21% O2. After G21 exposure, mothers were allowed to birth under normal housing conditions. Offspring were grown to 8 weeks under normal housing conditions.
|
| Growth protocol |
Pregnant dams were exposed to intermittent normoxia or intermittent hypoxia from G10-G21. Pups were born under normal housing conditions and allowed to grow to 8 weeks.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Microglia were immunomagentically isolated using Miltenyi anti-cd11b antibody. Microglia were lysed in trizol.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
MHV_S15
|
| Data processing |
Base calls made using Illumina 1.9 Software
Alignment made using Tophat v2.1
Raw counts generated using htseq-count --stranded reverse option
Filtered and normalized using EdgeR
GLM applied to count data and tagwise LRT performed using EdgeR
Differential expression calculated using decideTestDGE(lrt) in EdgeR
Genome_build: rn6
Supplementary_files_format_and_content: tab delimited txt files with raw counts
|
| |
|
| Submission date |
Dec 20, 2019 |
| Last update date |
Jul 13, 2020 |
| Contact name |
Andrea C Ewald |
| Organization name |
University of Wisconsin - Madison
|
| Department |
Comparative Biomedical Sciences
|
| Lab |
Watters
|
| Street address |
2015 Linden Dr
|
| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53706 |
| Country |
USA |
| |
|
| Platform ID |
GPL18694 |
| Series (1) |
| GSE142478 |
Sex- and region-specific transcriptomic differences in brainstem and cervical spinal cord microglia in rat offspring exposed to gestational intermittent hypoxia |
|
| Relations |
| BioSample |
SAMN13663618 |
| SRA |
SRX7427185 |
