Saturated fatty acid regulated lncRNA dataset during in vitro human embryonic neurogenesis

Human embryonic stem cells (hESCs) were used as a model of embryonic neurogenesis to identify the effect of excess fat uptake on neurodevelopment (Ardah et al., 2018). Herein, by directed differentiation of hESCs into neurons using established protocols, this data was generated for expression profiles of select lncRNAs during in vitro embryonic neurogenesis and their differential expression due to excess fat (palmitate) uptake. The undifferentiated hESCs were treated with 250 µM palmitate after identifying it as the highest concentration which is non-toxic to these cells. The palmitate treated hESCs were differentiated towards neurons keeping the levels of palmitate consistent throughout the differentiation process and fat uptake was confirmed by Oil Red O staining. The expression analysis of lncRNAs was performed by RT-qPCR on vehicle control and palmitate treated cells from 4 stages of differentiation, D0 (undifferentiated hESCs), D12 (neural stem cells), D44 (neural progenitors) and D70 (neurons) using lncRNAs array plates from Arraystar Inc. which contains 372 functionally identified lncRNAs found to be associated with lipid metabolism and other pathways (Cat# AS-NR-004).


a b s t r a c t
Human embryonic stem cells (hESCs) were used as a model of embryonic neurogenesis to identify the effect of excess fat uptake on neurodevelopment (Ardah et al., 2018). Herein, by directed differentiation of hESCs into neurons using established protocols, this data was generated for expression profiles of select lncRNAs during in vitro embryonic neurogenesis and their differential expression due to excess fat (palmitate) uptake. The undifferentiated hESCs were treated with 250 mM palmitate after identifying it as the highest concentration which is non-toxic to these cells. The palmitate treated hESCs were differentiated towards neurons keeping the levels of palmitate consistent throughout the differentiation process and fat uptake was confirmed by Oil Red O staining. The expression analysis of lncRNAs was performed by RT-qPCR on vehicle control and palmitate treated cells from 4 stages of differentiation, D0 (undifferentiated hESCs), D12 (neural stem cells), D44 (neural progenitors) and D70 (neurons) using lncRNAs array plates from Arraystar Inc. which contains 372 functionally identified lncRNAs found to be associated with lipid metabolism and other pathways (Cat# AS-NR-004 Value of the data This is the first data to show expression profile of several functionally identified lncRNAs in a human model of embryonic neurogenesis. The data was generated to find differential expression of particular lncRNAs due to treatment with excess fat (palmitate). Thus this data could be studied further to understand their effect on cellular metabolism or other biological processes during embryonic neurogenesis.
Since gene targets and biological processes/disease association of many of these lncRNAs is known, this data can be used to study the mechanism of action of particular lncRNAs in pathology, especially metabolic diseases in other models of metabolic syndrome.

Data
In this dataset, human embryonic stem cells (hESCs) were used as a model of embryonic neurogenesis. By their directed differentiation into neurons using established protocols [1][2][3], the expression profiles of select lncRNAs were assessed during in vitro embryonic neurogenesis (Fig. 3) and dataset was generated for differentially expressed lncRNAs due to excess fat uptake (Supplementary Table 1). The undifferentiated hESCs were treated with 250 mM palmitate after identifying it as the highest concentration which is non-toxic to these cells (Fig. 1) as this could lead to maximum effect of fat uptake without affecting cell viability. The palmitate treated hESCs were differentiated towards neurons in constant levels of palmitate throughout and fat uptake was confirmed by Oil Red O staining ( Fig. 2A and B). The expression analysis of lncRNAs was performed by RT-qPCR on vehicle control and palmitate treated cells from 4 stages of differentiation, D0 (undifferentiated hESCs), D12 (neural stem cells), D44 (neural progenitors) and D70 (neurons) using lncRNAs array plates from Arraystar Inc. which contains 372 functionally identified lncRNAs found to be associated with lipid metabolism and other pathways (Cat# AS-NR-004). Fig. 3 shows data on expression profile of these lncRNAs whereas Supplementary Table 1 contains list of these lncRNAs differentially expressed in the presence of palmitate (250 mM) relative to vehicle control at D0, D12, D44 and D70 of neural differentiation.

Cell culture and fat uptake
The undifferentiated hESCs (H9 cells) were cultured in feeder free condition on Matrigel coated 24-well tissue culture plates (Corning, Cat. # 3527) in mTesR1 media with palmitate treatment as described [1,4].

Expression analysis of lncRNAs
The expression analysis of lncRNAs was performed on palmitate treated and vehicle control cells from four stages of neural differentiation of hESCs, D0, D12, D44 and D70 using Long non-coding RNAs (lncRNAs) array plates were purchased from Arraystar, Inc. -USA (Cat# AS-NR-004) as described [1].

Oil Red O staining
To detect lipid uptake by cells at different time points of neural differentiation, 4-well plates containing cells treated with palmitate or vehicle control at D0 to D70 were stained with Oil Red O (Sigma, Cat# O0625) and quantified as published [1,5,6].