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Sample GSM3034738 Query DataSets for GSM3034738
Status Public on Mar 14, 2018
Title control_[noLPA]_replicate1 (2h time point)
Sample type RNA
 
Source name control_replicate1_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)

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
A_21_P0000744 11.919121
A_23_P110167 11.191984
A_33_P3414202 9.519057
A_33_P3263061 13.335061
A_24_P278460 9.723521
A_21_P0014651 7.377655
A_24_P286898 9.489743
A_23_P109034 10.359509
A_33_P3402035 11.673471
A_23_P11543 9.995394
A_21_P0014120 10.435657
A_21_P0014626 12.497508
A_23_P203658 9.154995
A_23_P206140 6.118148
A_33_P3241482 13.108231
A_23_P145541 9.493219
A_23_P144096 8.428808
A_24_P355944 14.233611
A_23_P203191 9.25127
A_23_P98183 11.521241

Total number of rows: 10605

Table truncated, full table size 235 Kbytes.




Supplementary file Size Download File type/resource
GSM3034738_US45102998_253949411849_S01_GE1_107_Sep09_1_1.txt.gz 3.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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