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Sample GSM819988 Query DataSets for GSM819988
Status Public on Oct 02, 2012
Title Hepatoblast Derived iPSC HB-iPSC1
Sample type RNA
 
Source name Hepatoblast Derived iPSC
Organism Mus musculus
Characteristics cell type: Hepatoblast Derived iPSC
genetic background: C57BL/6
Treatment protocol HB isolated from a pool of fetal (ED16.5) livers were purified using MACS system and hepatoblast-specific E-cadherin antibody. The cells were cultured in 100-mm dish at 75% confluence and transfected with a mixture of DNA containing 4 μg of pLentG-KOSM, 3.5 μg of pCMV-VSVG, and 2 μg of psPAX2 by Fugene HD. Twenty-four hours after transfection, the supernatant of transfected cells was collected and filtered through a 0.45 μm pore-size filter. The filtered lentiviral particles were concentrated by ultracentrifugation. For virus infection, mouse embryonic fibroblast (MEF) and mouse hepatic lineage cells were seeded in a 6-well plate at 1 × 105 cells per well one day before transduction. The medium was replaced with virus-containing supernatant, incubated for 2-3 hr and then cultured up to 7days with fresh media. For iPSC induction, the infected cells were trypsinized at day 7, plated in 1:5 ratio into six well plates containing feeder cells and incubated until appearance of ES-like cells.
Growth protocol All experiments were conducted according to the National Institutes of Health (NIH) guidelines for animal care and following a study protocol approved by the National Cancer Institute (NCI) Animal Care and Use Committee. Mice had free access to food and water.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted with Quiagen Rneasy Kit. Quality control and measurement were performed using NanoDrop and Agilent Bioanalyser.
Label biotin
Label protocol Biotinylated cRNA were prepared with the Ambion Totalprep RNA Amplification kit for Illumina arrays
 
Hybridization protocol Standard Illumina hybridization protocol
Scan protocol Standard Illumina scanning protocol
Description iPSC
replicate 1
Data processing Data was processed by using Gene Expression Module v 1.1.1 in Genome Studio V2009.1 from illumina, Inc. The background noise was substrated and quantile normalization was applied.
 
Submission date Oct 20, 2011
Last update date Oct 02, 2012
Contact name Daekwan Seo
E-mail(s) daekwan_seo@nih.gov
Phone 301-496-5688
Fax 301-496-0734
Organization name NIH
Department NCI
Lab LEC
Street address 37 Convent Dr. Rm 4140
City Bethesda
State/province MD
ZIP/Postal code 20878
Country USA
 
Platform ID GPL6885
Series (1)
GSE33110 Differentiation stage-specific donor memory in induced pluripotent stem cells (iPSC) generated from hepatic lineage cells

Data table header descriptions
ID_REF
VALUE Quantile normalized without background noise
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_2896528 2046.12 0
ILMN_2721178 345.4191 0
ILMN_3033922 235.0087 0
ILMN_3092673 1454.204 0
ILMN_2816356 35.20538 0.003759399
ILMN_2808939 1069.433 0
ILMN_2634564 524.3458 0
ILMN_2737647 -0.1508725 0.4172932
ILMN_2734484 626.2201 0
ILMN_2952292 45.2328 0.001253133
ILMN_2699078 -6.691414 0.7531328
ILMN_1213681 331.6736 0
ILMN_2735413 6.020489 0.2042606
ILMN_2735415 9.631005 0.1190476
ILMN_2891688 660.4066 0
ILMN_2637698 871.749 0
ILMN_2674228 685.4127 0
ILMN_2601546 17.07119 0.03634085
ILMN_1230831 8.154875 0.1491228
ILMN_2848071 21.67663 0.02255639

Total number of rows: 25697

Table truncated, full table size 739 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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