|
| Status |
Public on May 22, 2024 |
| Title |
control diet, liver endothelial cells, biol rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
liver
|
| Organism |
Mus musculus |
| Characteristics |
tissue: liver
cell type: sorted endothelial cells
treatment: control diet
treatment duration: 1 month
strain: C57BL6
|
| Treatment protocol |
Mice were kept on control or PLX5622 (1200 ppm) diet for one month
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Mice were anesthetized with ketamine/xylazine and decapitated. One lobe of the liver was dissected. A series of enzymatic and mechanical steps was used to achieve a single cell suspension of the liver tissue. FACS was used to enrich for CD31+ endothelial cells, which were sorted into trizol for RNA extraction. RNA was extracted using the RNeasy Micro kit from Qiagen
Non-stranded mRNA libraries were made using Illumina's TruSeq RNA Library Prep Kit v2 according to manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw paired-end sequencing data were aligned to the mouse genome (mm39 – UCSC Genome Browser) using STAR (v2.7.10a).
Gene counts were obtained using the featureCounts function from the R package Subread (v2.0.1).
Differential expression analysis was performed using default settings with DESeq2 (v1.32.0) in R (v4.1.0).
Assembly: mm39
Supplementary files format and content: excel file contains TPM values as well as DESeq2 statistics results
|
| |
|
| Submission date |
May 15, 2024 |
| Last update date |
May 22, 2024 |
| Contact name |
Caterina Profaci |
| Organization name |
University of California, San Diego
|
| Street address |
9500 Gilman Drive
|
| City |
La Jolla |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE267594 |
Microglia are not necessary for maintenance of blood-brain barrier properties in health, but PLX5622 alters brain endothelial cholesterol metabolism (Liver Seq) |
|
| Relations |
| BioSample |
SAMN41412023 |
| SRA |
SRX24569777 |
