|
| Status |
Public on Oct 01, 2018 |
| Title |
bp-ppar_3 |
| Sample type |
SRA |
| |
|
| Source name |
bp-ppar_3
|
| Organism |
Mus musculus |
| Characteristics |
treatment: vehicle
|
| Treatment protocol |
Cre (WT) or PPARg KO macrophages were treated with BSA-PBS and palm-LPS (doses above) for 8h
|
| Growth protocol |
thioglycolate peritoneal macrophages were islated day 4 after TG injection and plated. The next day the cells were stimulated as described below.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extraced using Ambion column kits.
Clonetech SMARTer v1
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq 2.0
Technical replicate fastq files were combined and aligned with STAR 2.0.4b
Gene counts dervied with Subread:featureCount 1.45 and annotated with Ensembl Biomart. RPKM calculated from gene counts with standard RPKM transformation with custom R scripting.
Genome_build: Ensembl GRCm38.76
Supplementary_files_format_and_content: Gene counts in tab-delimitted tex format
|
| |
|
| Submission date |
Jul 13, 2018 |
| Last update date |
Oct 01, 2018 |
| Contact name |
Joel D Schilling |
| E-mail(s) |
jschilli@dom.wustl.edu
|
| Phone |
314-747-8499
|
| Organization name |
Washington University School of Medicine
|
| Department |
Internal Medicine
|
| Lab |
Schilling lab
|
| Street address |
660 S. Euclid Ave
|
| City |
St. Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL21493 |
| Series (1) |
| GSE117115 |
PPARg Deficiency Suppresses the Release of IL-1b and a in Macrophages via a Type 1 Interferon Dependent Mechanism |
|
| Relations |
| BioSample |
SAMN09655923 |
| SRA |
SRX4390341 |
