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Sample GSM738126 Query DataSets for GSM738126
Status Public on May 22, 2012
Title hESC NSC 2
Sample type RNA
Source name neurosphere from hESC H9
Organism Homo sapiens
Characteristics sample type: neurosphere from hESC H9
gender: female
cell line: H9
treatment: hESC media lacking bFGF with TGF-b inhibitor and Noggin
Biomaterial provider SCIL
Treatment protocol hESC cultures were disaggregated using accutase for 10 min and plated on Matrigel-coated dishes in mTESR medium. hESC were allowed to expand for 3 d or until they were nearly confluent. The differentiation towards neural progenitors was performed in hESC media lacking bFGF with 10 µM TGF-b inhibitor (Tocris) and 500 ng/ml of Noggin (R&D). Upon day 5 of differentiation, the TGF-ß inhibitor was withdrawn while maintaining 500 ng/ml of Noggin and increasing amounts of N2 media (25%, 50%, 75%) was added for further 6 days with changing media for every 2 d.
Growth protocol neurosphere medium
Extracted molecule total RNA
Extraction protocol Rneasy (Qiagen)
Label biotin
Label protocol RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Using the Ambion WT Expression Kit, per sample, an amount of 100 ng of total RNA spiked with bacterial poly-A RNA positive controls (Affymetrix) was converted to double stranded cDNA in a reverse transcription reaction. Next the sample was converted and amplified to antisense cRNA in an in vitro transcription reaction which was subsequently converted to single stranded sense cDNA. Finally, samples were fragmented and labeled with biotin in a terminal labeling reaction according to the Affymetrix WT Terminal Labeling Kit.
Hybridization protocol A mixture of fragmented biotinylated cDNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix  GeneChip Human Gene 1.1 ST Array Plate followed by staining and washing in the GeneTitan® Instrument (Affymetrix) according to the manufacturer's procedures.
Scan protocol To assess the raw probe signal intensities, chips were scanned using the GeneTitan® HT Array Plate Scanner (Affymetrix).
Description neurospeheres derived from hESC
Data processing RMA-normalized expression values as obtained with the xps package (version 1.10.2) of BioConductor
Submission date Jun 07, 2011
Last update date May 23, 2012
Contact name Rekin's Janky
Organization name VIB
Department Nucleomics Core
Street address Herestraat 49 Box 816
City Leuven
ZIP/Postal code B-3000
Country Belgium
Platform ID GPL11532
Series (1)
GSE29770 Transduction of human fibroblasts with Zic3 combined with OCT4, SOX2 and KLF4 induces stable neural progenitor cell lines

Data table header descriptions
VALUE RMA-normalized expression values as obtained with the xps package (version 1.10.2) of BioConductor

Data table
7896736 6.409110856
7896738 3.174241813
7896740 3.233791448
7896742 9.410052727
7896744 5.285513191
7896746 9.067480075
7896748 5.487467055
7896750 3.174299347
7896752 10.94516581
7896754 7.788568265
7896756 4.501897677
7896759 7.01670802
7896761 5.506763776
7896779 6.93275806
7896798 6.063524514
7896817 5.91466019
7896822 9.398175051
7896859 4.389904044
7896861 3.563084895
7896863 4.493986707

Total number of rows: 28204

Table truncated, full table size 547 Kbytes.

Supplementary file Size Download File type/resource
GSM738126_hyb10336.CEL.gz 4.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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