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Sample GSM946324 Query DataSets for GSM946324
Status Public on Jun 11, 2012
Title ESC
Sample type RNA
Source name ESC
Organism Homo sapiens
Characteristics cell type: ES cells
Treatment protocol Undifferentiated human ESC and iPSC lines were cultured on mitotically-inactivated SNL feeder cells with Primate ES cell medium supplemented with 4 ng/ml bFGF. During the differentiation of the cells into macrophages, cells were cultured under 37°C , with 5% CO2 and 5% O2. On day 0, the iPSCs were plated at a ratio of 1:15 onto a mitotically-inactivated OP9 feeder layer on 100 mm cell culture plates in αMEM (Invitrogen) containing 10% FBS and 1% Antibiotic-Antimycotic (Invitrogen) supplemented with 50 ng/ml VEGFα (R&D Systems). On day 5, the medium was changed. On day 10, the differentiating iPSCs were collected by trypsinization, and Tra-1-85+ CD34+ and KDR+ hematopoietic progenitors were sorted on a FACS Aria II instrument (BD Biosciences). The progenitors were plated at 2 x 104 cells on another mitotically inactivated OP9 feeder layer on 100 mm cell culture plates or at 3 x 103 cells/well in 6 well cell culture plates in αMEM containing 10% FBS and 1% Antibiotic-Antimycotic supplemented with 50 ng/ml IL-3, 50 ng/ml SCF, 10 ng/ml TPO, 50 ng/ml FL and 50 ng/ml M-CSF (all R&D Systems). On day 18, the medium was changed. On day 26, differentiating cells were collected with Accumax (Innovative Cell Technologies), and CD14+ iPS-MPs were purified on an autoMACSpro instrument (Miltenyi Biotec).
Growth protocol We expanded the fibroblasts in DMEM (Nacalai tesque) containing 10% FBS (Invitrogen) and 0.5% penicillin and streptomycin (Invitrogen). To generate iPS cells, we introduced OCT3/4, SOX2, KLF4 and c-MYC by using ecotropic retroviral transduction into fibroblasts expressing the mouse Slc7a1 gene. Six days after transduction, the cells were harvested and re-plated onto mitotically inactivated SNL feeder cells. The next day, we replaced the medium with Primate ES cell medium (ReproCELL) supplemented with 4 ng/ml bFGF (Wako). Three weeks after this period, individual colonies were isolated and expanded. Cell culture was performed under 37°C , with 5% CO2 and 21% O2.
Extracted molecule total RNA
Extraction protocol Total RNA was column-purified with the RNeasy kit (Qiagen) and treated with RNase-free DNase (Qiagen).
Label Cy3
Label protocol 20 µg of total RNA was first amplified with WT-OvationTM Pico System (Nugen). The RNA was labelled with Cy3 using Genomic DNA Enzymatic Labeling Kit (Agilent Technologies).
Hybridization protocol Labelled cDNA was fragmented with Gene Expression Hybridization Kit (Agilent Technologies), followed by hybridization at 65˚C for 17 hrs.
Scan protocol Images were acquired by DNA Microarray Scanner (Agilent Technologies)
Description ES cells which was previously established
Data processing Raw data were processed with FeatureExtraction version 10.7. Background signal was subtracted.
Submission date Jun 10, 2012
Last update date Jun 11, 2012
Contact name Akira Watanabe
Organization name Kyoto University
Department Medical Innovation Center
Street address Shogoin-Kawahara-cho 53, Sakyo-ku
City Kyoto
State/province Kyoto
ZIP/Postal code 606-8507
Country Japan
Platform ID GPL13607
Series (1)
GSE38626 Induced pluripotent stem cells from CINCA syndrome patients as a model for dissecting somatic mosaicism and drug discovery

Data table header descriptions
VALUE processed Cy3 signal intensity (Agilent gProcessedSignal)

Data table
1 1.012240e+004
2 2.478137e+000
3 2.493467e+000
4 8.036001e+001
5 5.322132e+001
6 5.192862e+001
7 7.806106e+002
8 5.325326e+002
9 2.557602e+000
10 2.276441e+001
11 2.571120e+000
12 2.161518e+001
13 5.196992e+002
14 4.509230e+001
15 8.419177e+003
16 3.742175e+002
17 7.804871e+000
18 2.590501e+000
19 2.590141e+000
20 1.246802e+002

Total number of rows: 62976

Table truncated, full table size 1219 Kbytes.

Supplementary file Size Download File type/resource
GSM946324_khES3-ESCraw.txt.gz 3.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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