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Sample GSM738127 Query DataSets for GSM738127
Status Public on May 22, 2012
Title hESC 3
Sample type RNA
Source name hESC H9
Organism Homo sapiens
Characteristics cell type: hESC H9
gender: female
cell line: H9
Biomaterial provider WiCell, Madison, WI
Treatment protocol cultured for two passages on matrigel in mTESR medium
Growth protocol mTESR 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 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 5.938071677
7896738 3.300371232
7896740 3.057951013
7896742 9.296227953
7896744 4.605174279
7896746 9.40814289
7896748 6.054677027
7896750 3.315887888
7896752 11.12163064
7896754 7.497308978
7896756 4.297448232
7896759 5.406203304
7896761 5.042070822
7896779 7.458595269
7896798 6.194764733
7896817 5.898829903
7896822 9.141596278
7896859 4.470413219
7896861 3.665858888
7896863 4.979097032

Total number of rows: 28204

Table truncated, full table size 547 Kbytes.

Supplementary file Size Download File type/resource
GSM738127_hyb10339.CEL.gz 4.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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