|
| Status |
Public on Nov 24, 2023 |
| Title |
adipocyte-siControl-3 |
| Sample type |
RNA |
| |
|
| Source name |
Primary adipocyte culture, 4 days after siRNA treatment
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Adipocyte
genotype: control
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using Macherey-Nagel nucleospin RNA silica membrane purification kit REF740955
|
| Label |
biotin
|
| Label protocol |
100 ng of total RNA was used to generate amplified sense strand cDNA targets using GeneChip® WT Plus Reagent Kit (ThermoFisher Scientific) followed by fragmentation and labelling
|
| |
|
| Hybridization protocol |
2.3 µg of ss cDNA target was hybridized to Clariom™ S Human Arrays for 16 hours at 45°C under rotation in Affymetrix Gene Chip Hybridization Oven 645 (ThermoFisher Scientific)
|
| Scan protocol |
Washing and staining was carried out on Affymetrix GeneChip® Fluidics Station 450 (ThermoFisher Scientific), according to the manufacturer’s protocol. The fluorescent intensities were determined with Affymetrix GeneChip Scanner 3000 7G (ThermoFisher Scientific). For image processing software AGCC 4.0 was used.
|
| Data processing |
Microarray data were analyzed with packages available from R Bioconductor (http://www.bioconductor.org), R version 4.2.0. Normalization and calculation of gene expression were performed with the Robust Multichip Average expression measure using the oligo package. Before further analysis, a nonspecific filter was applied to include only coding genes with log2 expression signal > 5 in at least 50% of all samples. To identify differentially expressed genes, the remaining 26787 transcripts were analyzed using the Linear Models for Microarray Data (limma) package (version 3.52.2) between two groups. Adjusted P value was used for statistical significance.
|
| |
|
| Submission date |
Nov 15, 2023 |
| Last update date |
Nov 24, 2023 |
| Contact name |
Niklas Mejhert |
| E-mail(s) |
niklas.mejhert@ki.se
|
| Organization name |
Karolinska Institute
|
| Street address |
Blickagången 16
|
| City |
Huddinge |
| ZIP/Postal code |
141 52 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL23159 |
| Series (2) |
| GSE247813 |
Transcriptional determinants of lipid mobilization in human adipocytes [Microarray] |
| GSE247818 |
Transcriptional determinants of lipid mobilization in human adipocytes |
|
