|
Status |
Public on Jul 13, 2020 |
Title |
female normoxia cervical cord replicate 2 [FNV_S22] |
Sample type |
SRA |
|
|
Source name |
female normoxia cervical cord
|
Organism |
Rattus norvegicus |
Characteristics |
strain: sprague dawley Sex: female air treatment: normoxia 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 |
FNV_S22
|
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 |
SAMN13663624 |
SRA |
SRX7427187 |