|
| Status |
Public on Apr 28, 2022 |
| Title |
GapmeR against ADIPINT 2 replicate4 |
| Sample type |
RNA |
| |
|
| Source name |
hADSC
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Adipose Derived Stem Cells (hADSC)
group: GapmeR 2
|
| Treatment protocol |
Antisense LNA GapmeRs (Qiagen) were introduced by electroporation using a Neon Transfection System (1300 V, 20 ms, 2 pulses) 100 µL Kit (Invitrogen) in human in vitro differentiated hADSCs at day eight of differentiation.
|
| Growth protocol |
hADSC cells were plated at a cell density of 20 000 cells/cm2 and incubated at 37°C with 5% CO2. Adipogenesis was induced two days post confluence using DMEM/F12 as well as the adipogenic cocktail; 5 mg/mL insulin, 0.25 mmol/l dexamethasone, 0.5 mmol/l 3-isobutyl-1-methylxanthine (IBMX) and 10 mmol/l rosiglitazone for two days after which the dexamethasone and IBMX were removed and the cells were allowed to undergo full adipogenic differentiation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the NucleoSpin RNA kit (Macherey-Nagel, cat. 740955.250) according to the manufacture's instructions. The concentration, purity and quality were measured using Nanodrop 2000 (Thermo Fisher Scientific) and Agilent 2100 Bioanalyzer (Agilent Technologies).
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA was prepared using the GeneChip WT Plus Reagent Kit according to the standard Affymetrix protocol from 150ng total RNA.
|
| |
|
| Hybridization protocol |
5 ug fragmented and biotinylated ssDNA were hybridized for 16 hr at 45C to Affymetrix Clariom S human arrays according to standard protocol. Washing and staining were performed using Affymetrix Fluidics Station 450.
|
| Scan protocol |
The fluorescent intensities were determined with Affymetrix GeneChip Scanner 3000 7G
|
| Data processing |
Data were preprocessed and analyzed using the Affymetrix Expression Console (version 1.4.1) and standard SST-RMA method. Prior to further analysis, collapseRows R function (Miller et al., 2011) was used to convert and collapse the transcript abundance quantification detected by Affymetrix probe sets to mapped FANTOM-CAT IDs. Affymetrix probe IDs were mapped to the FANTOM-CAT gene model , 54,980 probe sets mapped to 40,590 unique gene IDs.
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| |
|
| Submission date |
Mar 21, 2022 |
| Last update date |
Apr 28, 2022 |
| Contact name |
hui Gao |
| E-mail(s) |
hui.gao@ki.se
|
| Organization name |
Karolinska Institutet
|
| Department |
Department of Biosciences and Nutrition
|
| Street address |
Novum
|
| City |
Huddinge |
| ZIP/Postal code |
14183 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL23126 |
| Series (1) |
| GSE199076 |
The long noncoding RNA ADIPINT is a gatekeeper of pyruvate carboxylase function regulating human fat cell metabolism |
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