|
| Status |
Public on Sep 15, 2020 |
| Title |
CDAA mLSEC, biological rep3 |
| Sample type |
RNA |
| |
|
| Source name |
Primary murine liver sinusoidal endothelial cells after 10 weeks of CDAA diet, biological replicate no 3
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Primary liver sinusoidal endothelial cells
treatment: CDAA diet
treatment duration: 10 days
|
| Treatment protocol |
Livers were perfused in situ through the portal vein with a collagenase/amino acid/saccharide solution (Sigma-Aldrich), dissected, mechanically disrupted, pooled from 3 mice, digested for 25 minutes at 38 °C in collagenase/Gey’s balanced salt solution (Sigma-Aldrich), and filtered through a mesh. Nonparynchymal cells were separated by a 19.3% Nycodenz gradient. Afterward, liver sinusoidal endothelial cells (LSEC) were isolated by Magnetic-activated cell sorting (MACS) using CD146 MicroBeads (Miltenyi) according to manufacturers’ instructions.
|
| Growth protocol |
Ten-week-old female C57BL/6N mice and control siblings were fed a CDAA diet containing 31% of fat per calorie and 1% cholesterol (E15666-94, Ssniff) or a control diet (V1534-000, Ssniff) for ten weeks.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with innuPREP RNA Mini Kit (Analytik Jena), then treated with TURBO DNA-free Kit (Invitrogen).
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol.
|
| |
|
| Hybridization protocol |
Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.
|
| Scan protocol |
Affymetrix GeneArray Scanner3000.
|
| Description |
CDAA3
Gene expression data of primary murine liver sinusoidal endothelial cells after 10 weeks of CDAA diet, biological replicate no 3
|
| Data processing |
The data were analyzed with a commercial software called JMP Genomics, version 8, from SAS. Gene expression profiling was performed using arrays of mouse Mogene-2_0-type from Affymetrix. A Custom CDF Version 22 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary.
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| |
|
| Submission date |
Nov 25, 2019 |
| Last update date |
Sep 16, 2020 |
| Contact name |
Carsten Sticht |
| Organization name |
University Heidelberg
|
| Department |
ZMF
|
| Street address |
Theodor-Kutzer-Ufer
|
| City |
Mannheim |
| ZIP/Postal code |
68169 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24557 |
| Series (2) |
| GSE140994 |
Expression data of primary murine liver sinusoidal endothelial cells after 10 weeks of CDAA diet |
| GSE141004 |
Expression data of murine liver sinusoidal endothelial cells |
|
