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Sample GSM738121 Query DataSets for GSM738121
Status Public on May 22, 2012
Title hESC 1
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 6.286511558
7896738 3.110057499
7896740 3.14843794
7896742 9.628451008
7896744 4.689192912
7896746 9.690207549
7896748 5.684137055
7896750 3.12763328
7896752 10.42622282
7896754 7.290728497
7896756 4.517546567
7896759 5.610738444
7896761 5.545934401
7896779 7.394942799
7896798 6.16606263
7896817 5.661664103
7896822 9.089702054
7896859 4.534098965
7896861 4.088853947
7896863 5.159088235

Total number of rows: 28204

Table truncated, full table size 547 Kbytes.

Supplementary file Size Download File type/resource
GSM738121_hyb10327.CEL.gz 4.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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