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Sample GSM738122 Query DataSets for GSM738122
Status Public on May 22, 2012
Title Zic3 NPC1
Sample type RNA
Source name ZiNPC
Organism Homo sapiens
Characteristics cell type: ZiNPC derived from BJ1 fibroblasts
gender: male
cell line: BJ1
treatment: Zic3, KLF4, OCT4 and SOX2
Biomaterial provider SCIL
Treatment protocol The coding region of the mouse Zic3 gene was amplified by RT-PCR and cloned in pMIG-IRES-GFP plasmid (Addgene). The pMXs plasmids encoding for OCT4, SOX2 and KLF4 were purchased from Addgene. pMXs and pMIG-based retroviral vectors were transfected individually along with the viral packaging genes gag-pol (Addgene) and VSVG (Addgene) into 293T cells (ATCC) using Fugene HD reagent (Roche) according to the manufacturer's directions. Human BJ1 cells (Lonza) were seeded at 1.5 x 105 cells/well in 6-well plates (Sigma) without feeders. Cells were transduced with Zic3, KLF4, OCT4 and SOX2 retroviral vector containing supernatants mixed equally. To achieve maximum transduction efficiency, cells were transduced twice with the viral supernatant. Four days after transduction, the transduced cells were reseeded at 1.5 x 105 cells per 100-mm dish containing MEF and cultured with hESC medium. ZiNPC were picked in 15-20 days post transduction.
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 BJ1 fibroblast transduced with OCT4, SOX2, KLF4 and Zic3
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 6.792256708
7896738 3.217534736
7896740 3.091236066
7896742 9.685495193
7896744 5.52672614
7896746 8.64141236
7896748 5.727822457
7896750 3.180653925
7896752 10.09875588
7896754 8.569551851
7896756 4.502585202
7896759 6.570437125
7896761 6.426536493
7896779 8.218044911
7896798 6.169646454
7896817 5.869533389
7896822 8.356685248
7896859 4.57345936
7896861 3.716738538
7896863 5.317604357

Total number of rows: 28204

Table truncated, full table size 547 Kbytes.

Supplementary file Size Download File type/resource
GSM738122_hyb10328.CEL.gz 4.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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