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Sample GSM3405936 Query DataSets for GSM3405936
Status Public on Dec 01, 2018
Title RNA-seq, Primary stromal cells from BM adipocyte diff 9d donor 1
Sample type SRA
Source name Primary stromal cells from BM adipocyte diff 9d
Organism Homo sapiens
Characteristics cell line: Primary stromal cells from BM
differentiation status: adipocyte
timepoint: 9d
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 Both induction cocktails were replaced every third day, while dexamethasone and isobutylmethylxanthine were withdrawn at day three and rosiglitazone at day 6 of adipogenic differentiation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 HiSeq 1500
Description BM_Ad_1
Data processing Quality of all libraries were assessed using FastQC ( /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: raw and normalized gene counts with statistics
Submission date Sep 28, 2018
Last update date Dec 01, 2018
Contact name Susanne Mandrup
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 GPL18460
Series (1)
GSE113253 Osteogenesis depends on commissioning of a network of stem cell transcription factors that act as repressors of adipogenesis
BioSample SAMN10142204

Supplementary data files not provided
Processed data are available on Series record
Raw data not provided for this record

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