|
| Status |
Public on Sep 06, 2018 |
| Title |
KO Rep3_DMSO |
| Sample type |
SRA |
| |
|
| Source name |
KO_DMSO_Thioglycollate-elicited peritoneal macrophages
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
age: 8.5 weeks
genotype/variation: PPARgammaMPKO
cell type: Thioglycollate-elicited peritoneal macrophages
|
| Treatment protocol |
After overnight culture, macrophages were untreated or treated with 20ng/mL IL4, or 1uM Rosi or equal volume of DMSO as vehicle control.
|
| Growth protocol |
Control and PPARgMKO mice were injected with 3% thioglycollate into the peritoneal cavity. 4 days post injection the ellicited macrophages were harvested and cultured overnight in DMEM.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After treatment, cells were immediately lysed in trizol and RNA purified with RNeasy RNA isolation kit according to the manufacturers instructions. Illumina Truseq Stranded RNA Total RNA library prep kit was used with 1ug RNA of total RNA for construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
15_KO_DMSO
KO_DMSO_3
|
| Data processing |
#genome alignment: tophat2 -p 16 -g 1
#counting reads: featureCounts -t exon -g gene_id -a mm9.gtf
#DGE with edgeR
Genome_build: mm9
Supplementary_files_format_and_content: normlized FPKM of all samples
|
| |
|
| Submission date |
Feb 26, 2018 |
| Last update date |
Sep 06, 2018 |
| Contact name |
Hoang Nguyen |
| E-mail(s) |
hoang.buinguyen@pennmedicine.upenn.edu
|
| Phone |
(215) 898-0198
|
| Organization name |
University of Pennsylvania Perelman School of Medicine
|
| Street address |
3400 Civic Center Boulevard
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104-5160 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE111102 |
Transcriptional analysis of PPARgamma activation in control and PPARgamma null macrophages [RNA-seq] |
| GSE111105 |
Transcriptional analysis of PPARgamma activation in control and PPARgamma null macrophages |
|
| Relations |
| BioSample |
SAMN08606509 |
| SRA |
SRX3742020 |
