|
| Status |
Public on Jul 12, 2019 |
| Title |
Male Nx LPS 2 |
| Sample type |
SRA |
| |
|
| Source name |
P9 microglia
|
| Organism |
Rattus norvegicus |
| Characteristics |
treatment: male normoxia LPS
tissue: whole brain microglia
age: Postnatal day 9
|
| Treatment protocol |
Normoxia exposure consisted of 8 hours of room air (21% O2), intermittent hypoxia exposure consisted of expsosure to 2 min cycles of either 10.5% O2 or 21% for 8 hrs a day. At P9, 16 hours following the last IH exposure, pups were injected with either saline or 0.1 mg/mL LPS (i.p.)
|
| Growth protocol |
Neonates were exposed with dams in home cages to 8 days of normoxia or intermittent hypoxia starting at P1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Microglia were immunomagentically isolated using Miltenyi anti-cd11b antibody. Microglia were lysed in trizol.
RNA stranded libraries were prepared according Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
male normoxia LPS sample sample 2
|
| 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
Supplementary_files_format_and_content: csv files with normalized counts
|
| |
|
| Submission date |
Feb 22, 2019 |
| Last update date |
Jul 12, 2019 |
| Contact name |
Jyoti Watters |
| E-mail(s) |
jjwatters@wisc.edu
|
| Phone |
6082656092
|
| Organization name |
University of Wisconsin-Madison
|
| Department |
CBS
|
| Lab |
Jyoti Watters
|
| Street address |
2015 Linden Drive
|
| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53706 |
| Country |
USA |
| |
|
| Platform ID |
GPL18694 |
| Series (1) |
| GSE126946 |
Neonatal intermittent hypoxia exposure sex-specifically augments rat microglial cytokine expression acutely and long-term |
|
| Relations |
| BioSample |
SAMN10988820 |
| SRA |
SRX5409687 |
