|
| Status |
Public on Mar 14, 2018 |
| Title |
control_[noLPA]_replicate2 (2h time point) |
| Sample type |
RNA |
| |
|
| Source name |
control_replicate_2_2h
|
| Organism |
Homo sapiens |
| Characteristics |
Sex: female
cell type: neural progenitor cells (NPCs)
derived from: WA-09 (H9 HESC-line)
passage: rosette passaging number 2 (RP2)
time point: 2h
|
| Treatment protocol |
NPCs were cultured in 0.5 ml N2B27 + FGF2/EGF in 24-well plates without- or in the presence of LPA [25 uM] for 2h, 10h and 24h.
|
| Growth protocol |
NPCs were cultured in N2B27 + human FGF2 and mouse EGF. HESCs were differentiated into NPCs using a three-dimensional Dual SMAD signaling inhibitino protocol. NPCs were kept in 24-well plates with a daily medium change (N2B27 =FGF2/EGF medium)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the Qiagen Rneasy Mini Kit. RNA was DNAse treated and re-purified using the Qiagen Rneasy Mini Kit. RNAse quality was confirmed using Agilent Bioanalyzer.
|
| Label |
Cy3
|
| Label protocol |
RNA was used to reverse transcribe double stranded cDNA and subsequently in-vitro transcribe Cy3-labeled target cRNA with the Low Input Quick Amp Labeling Kit (Agilent Technologies).
|
| |
|
| Hybridization protocol |
The target cRNAs were hybridized to SurePrint G3 Human GE 8×60K Microarrays (AMADID 039494, Agilent Technologies).
|
| Scan protocol |
Scanned images were analysed with the Feature Extraction software 10.7.1.1 (Agilent Technologies) using default parameters (protocol: GE1_107_Sep09, grid: 039494_D_F_20120628) to obtain background-corrected signal intensities.
|
| Description |
Gene expression after 2 h (control)
|
| Data processing |
The data were further analysed with the GeneSpring GX Software (Version 13.0, Agilent Technologies), where quantile normalization of the data and removal of unreliable signal intensities (filtering of data by expression: in three out of six experiments the signal intensity of a probe had to be above the 20th percentile to be retained in the data set) were performed. For statistical analysis a one-way ANOVA analysis with a p-value cutoff of 0.05 was performed.
|
| |
|
| Submission date |
Mar 08, 2018 |
| Last update date |
Mar 14, 2018 |
| Contact name |
Jan-Philip Medelnik |
| E-mail(s) |
jan.medelnik@imp.ac.at
|
| Organization name |
Research Institute of Molecular Pathology (IMP)
|
| Lab |
Tanaka
|
| Street address |
Campus-Vienna-Biocenter 1
|
| City |
Vienna |
| State/province |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
| |
|
| Platform ID |
GPL17077 |
| Series (1) |
| GSE111597 |
Gene-expression analysis of human embryonic stem cell (HESC-)- derived rosette-forming neural progenitor cells (NPCs) in the presence of lysophosphatidic acid (LPA) |
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