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Sample GSM324165 Query DataSets for GSM324165
Status Public on Nov 07, 2008
Title hFSF-4PU-Pre-iPS-1_rep3
Sample type RNA
 
Source name Pre-iPS cell line derived from hFSF by 4F+p53si+UTF1, clone 1 (rep 3)
Organism Homo sapiens
Characteristics patial reprogrammed cells
Donor: hFSF
Growth protocol Human fibroblasts were cultured in Dulbecco’s Modified Eagle Medium (DMEM, Hyclone) containing 10% fetal bovine serum (FBS, Gibco). hES cells, iPS cells and Pre-iPS cells were maintained on Mitomycin C-treated MEFs in hES Cell culture medium consisting of 80% DMEM/F12 (Invitrogen), 20% Knockout serum replacement (KSR) (Invitrogen), 1 mM L-glutamine, 1% non-essential amino acids, 0.1 mM beta-mercaptoethanol (all from Invitrogen) and 4 ng/ml basic fibroblast growth factor bFGF (P&A Biotech).
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from cells using TRIzol (Invitrogen) according to the manufacturer’s protocol.
Label Cy5
Label protocol cDNA were synthesized by reverse transcription using the Amino Allyl MessageAmp II aRNA Amplification kit (Ambion) with oligo(dT) primer that contain a T7 RNA polymerase promoter sequence, according to the manufacturer’s instruction. In vitro transcription was then performed with the purified cDNA and amino allyl UTP was incorporated during transcription to produce amino allyl modified aRNA that was subsequently coupled to cy5 dye label by reacting at 25℃ for 2h.
 
Hybridization protocol The Human OneArray was hybridized using 1.5× OneArrayTM Hybridization Buffer for 16 h at 60℃; then washed in Wash Buffer 1, 2 and 3 accroding to the manufacturer's instruction.
Scan protocol Arrays were scanned using GenePix 4000B scanner (Molecular Devices) according to the manufacturer’s protocol
Description gene expression comparation of iPS production, 4F represents OCT4/SOX2/c-Myc/KLF4
Data processing After removing control probes, a 14/33 presence call (SNR>=5 and foreground-background>0) was used to filter probes for the 33 microarrays, resulting in 12311 probes for further quantile normalization. The median of each sample was used for hierarchical clustering. Complete-linkage hierarchical clustering was performed using cluster 3.0 with Spearman rank correlation coefficient as gene distances measurement, and Pearson correlation coefficient as sample distances measurement (Attached in supplementary data).
 
Submission date Sep 24, 2008
Last update date Nov 07, 2008
Contact name hongkui deng
E-mail(s) hongkui_deng@pku.edu.cn
Phone 86-10-6275-6474
Fax 86-10-6275-6474
Organization name Peking University
Department College of Life Sciences
Street address Yiheyuan Road 5#, Haidian District
City Beijing
ZIP/Postal code 100871
Country China
 
Platform ID GPL6254
Series (1)
GSE12922 Two Supporting Factors Greatly Improve the Efficiency of Human iPS Cell Generation

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
PH_hs_0016855 1571.2
PH_hs_0004792 679.7
PH_hs_0034114 353.6
PH_hs_0014268 228.9
PH_hs_0025404 2509.4
PH_hs_0019562 1037.7
PH_hs_0001556 2404.6
PH_hs_0028077 368.5
PH_hs_0006095 142.6
PH_hs_0023839 469.0
PH_hs_0024947 336.1
PH_hs_0036879 208.5
PH_hs_0003980 98.3
PH_hs_0004749 856.2
PH_hs_0032989 6103.0
PH_hs_0014799 1488.9
PH_hs_0024958 3175.5
PH_hs_0037858 4550.1
PH_hs_0001375 2471.1
PH_hs_0024975 354.7

Total number of rows: 12773

Table truncated, full table size 254 Kbytes.




Supplementary file Size Download File type/resource
GSM324165.gpr.gz 2.9 Mb (ftp)(http) GPR
Processed data included within Sample table

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