|
| Status |
Public on Dec 01, 2018 |
| Title |
RNA-seq, HEK293 osteoblast diff 7d |
| Sample type |
SRA |
| |
|
| Source name |
HEK293 osteoblast diff 7d
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293
differentiation status: osteoblast
timepoint: 7d
|
| Treatment protocol |
Immortalized cells and non-mesenchymal cells: Two days post confluency cells were induced to undergo osteoblast or adipocyte differentiation by switched to α-MEM supplemented with 10% FCS, 10 mM dexamethasone, 10 nM vitamin D, 10 mM β-glycerolphosphate, and 50 µg/ml ascorbic acid or to DMEM supplemented with 10% fetal serum, 10ug/mL insulin, 1µM rosiglitazone, 100 mM dexamethasone, and 500 µM isobutylmethylxanthine. Media was replaced on day 2, 4, 7, 9 and 11.
Human primary stromal cells: Primary cells were expanded prior to the induction of differentiation with DMEM/F-12 supplemented with 10 % FCS, 1 % P/S, 15 mM HEPES and 1 nM FGF-1. Osteogenic induction was similar as for the immortalized cells while the adipogenic induction cocktail contained DMEM/F12 supplemented with 1 % P/S, 15 mM HEPES, 500 µM isobutylmethylxanthine, 100 nM dexamethasone, 10 µg/mL insulin and transferrin, 2 nM T3 and 200 mM rosiglitazone. Both induction cocktails were replaced every third day, while dexamethasone and isobutylmethylxanthine were withdrawn at day three and rosiglitazone at day 6 of adipogenic differentiation
|
| Growth protocol |
Telomerase-immortalized human mesenchymal stromal cells of bone marrow (BM-hMSC-TERT4) or adipose tissue origin (AT-hMSC-TERT) as well as non-mesenchymal cells were grown under standard cell culture conditions in α-MEM supplemented with 10 % fetal calf serum (FCS) and 1 % penicillin/streptomycin (P/S). Primary stromal cells were gron in DMEM/F12 supplemented with 15 mM HEPES, 10 % fetal calf serum (FCS) and 1 % penicillin/streptomycin (P/S)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA-seq: RNA was extracted from 6-well dishes using TRI Reagent (Sigma) follwed by chloroform extraction and purification of RNA using Econo Spin columns (Epoch Life Sciences).
RNA-seq was performed according to manufacturer’s instructions (TruSeq 2, Illumina) using 2 µg RNA for preparation of cDNA libraries.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
HEK293_Ob
RNA_NonMesenchymalCells.txt
|
| Data processing |
Quality of all libraries were assessed using FastQC (http://www.bioinformatics.babraham.ac.uk /projects/fastqc/).
RNA-seq reads were aligned to hg19 genome using STAR aligner and default settings. Only one read per position and read length was kept.
Genome_build: hg19
Supplementary_files_format_and_content: The txt file "RNA_NonMesenchymalCells.txt" contains only raw gene counts and normalized gene counts, but no log 2 fold changes or statistics due to lack of replicates.
|
| |
|
| Submission date |
Sep 28, 2018 |
| Last update date |
Dec 01, 2018 |
| Contact name |
Susanne Mandrup |
| E-mail(s) |
s.mandrup@bmb.sdu.dk
|
| Phone |
+45 6550 2340
|
| Organization name |
University of Southern Denmark
|
| Department |
Biochemistry and Molecular Biology
|
| Street address |
Campusvej 55
|
| City |
Odense M |
| ZIP/Postal code |
5230 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE113253 |
Osteogenesis depends on commissioning of a network of stem cell transcription factors that act as repressors of adipogenesis |
|
| Relations |
| BioSample |
SAMN10142186 |
| SRA |
SRX4774798 |
