|
| Status |
Public on May 15, 2016 |
| Title |
in vivo, KO 3 |
| Sample type |
SRA |
| |
|
| Source name |
Atherosclerosis lesion
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Mixture of cell types (SMC, Epithelial, Macrophage, others)
strain: C57BL/6
genotype: Oct4 -/-
treatment: Western Diet
oxygen levels: n/a
|
| Treatment protocol |
For in vivo, animals were maintened in a Western Diet for 18 weeks
For in vitro, cell
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For in vivo, BCA were removed and flash frozen and RNA was harvested using standar Trizol reagent/protocol.
For in vitro, RNA was harvested using standard Trizol reagent/protocol
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
oct4-atherosclerosis-in-vivo-rnaseq-rawcounts.txt
oct4-atherosclerosis-in-vivo-rnaseq-summary.txt
SL60370
|
| Data processing |
Basecalls performed using CASAVA
Data were aligned to the mm9 genome using STAR version 3.0
Aligned reads were counted against genes from the UCSC mm9 annotation using the featureCounts from the SubRead package
Data were normalized for library size using the DESeq2 median ration normalization procedure described in Ander and Huber (2010).
Differential gene expression was assessed using the DESeq2 package in R
Genome_build: mm9
Supplementary_files_format_and_content: Counts of reads aligning to genes from the mm9 annotation as output from featureCounts
|
| |
|
| Submission date |
Nov 16, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Gary K Owens |
| Organization name |
University of Virginia
|
| Street address |
415 Lane Road MR5 Building Room 1322
|
| City |
Charlottesville |
| State/province |
VA |
| ZIP/Postal code |
22908 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE75044 |
Activation of the pluripotency factor OCT4 in smooth muscle cells is atheroprotective. doi: 10.1038/nm.4109 |
|
| Relations |
| BioSample |
SAMN04271157 |
| SRA |
SRX1433536 |
