GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM3405949

Query DataSets for GSM3405949

Status

Public on Dec 01, 2018

Title

RNA-seq, A549 undifferentiated

Sample type

SRA

Source name

A549 undifferentiated

Organism

Homo sapiens

Characteristics

cell line: A549
differentiation status: undifferentiated
timepoint: n/a

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 Both induction cocktails were replaced every third day, while dexamethasone and isobutylmethylxanthine were withdrawn at day three and rosiglitazone at day 6 of adipogenic differentiation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

A549_Msc
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