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Status |
Public on Dec 01, 2018 |
Title |
RNA-seq, SHSY5Y adipocyte diff 7d |
Sample type |
SRA |
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Source name |
SHSY5Y adipocyte diff 7d
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Organism |
Homo sapiens |
Characteristics |
cell line: SHSY5Y differentiation status: adipocyte timepoint: 7d
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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 Both induction cocktails were replaced every third day, while dexamethasone and isobutylmethylxanthine were withdrawn at day three and rosiglitazone at day 6 of adipogenic differentiation
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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)
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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Description |
SH_SY5Y_Ad RNA_NonMesenchymalCells.txt
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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.
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Submission date |
Sep 28, 2018 |
Last update date |
Dec 01, 2018 |
Contact name |
Susanne Mandrup |
E-mail(s) |
s.mandrup@bmb.sdu.dk
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Phone |
+45 6550 2340
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Organization name |
University of Southern Denmark
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Department |
Biochemistry and Molecular Biology
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Street address |
Campusvej 55
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City |
Odense M |
ZIP/Postal code |
5230 |
Country |
Denmark |
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Platform ID |
GPL24676 |
Series (1) |
GSE113253 |
Osteogenesis depends on commissioning of a network of stem cell transcription factors that act as repressors of adipogenesis |
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Relations |
BioSample |
SAMN10142176 |
SRA |
SRX4774806 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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