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Sample GSM1033417 Query DataSets for GSM1033417
Status Public on Apr 15, 2013
Title in vitro derived definitive endoderm 3
Sample type RNA
 
Source name mESC
Organism Mus musculus
Characteristics strain: 129X1/SvJ x 129S1/SV-+p+Tyr- cKitlSl-J/+
tissue: in vitro derived definitive endoderm
sentrix_id: 8615501026
sentrix_position: C
Treatment protocol Mouse PSC Differentiation: Maintenance cultures were split and MEF depleted for 30 minutes in maintenance media. PSCs were collected and resuspended in differentiation media 1 [A-DMEM (GIBCO, 12491) supplemented with 1% N2 (GIBCO, 17502-048), 2% B27 minus vitamin A (GIBCO, 12587-010), 1% Glutamax (GIBCO, 35050079) 1% P/S (Cellgro, 30-001-CI)] and 10µM Y-27632 (Selleck Chemicals, S1049). Cells were plated at 5x103 cells/cm2 onto 0.1% gelatin-coated 6 well plates. On day 2 cells were fed with differentiation media 1 with 5nM GSKiXV (Calbiochem, 361558) and 5µM IDE-1 (Tocris, 4015). On days 3, 4, and 5, cells were fed with differentiation media 2 [A-DMEM (GIBCO, 12491) supplemented with 2% B27 minus vitamin A, 1% Glutamax, 1% P/S] plus 5µM IDE-1. On day 6 cultures were split with 0.25% trypsin and plated at 3x105 cells/cm2 onto 804G conditioned medium-coated plates with 10µM Y-27632 in differentiation media 2. Cells were treated with 500nM A83-01 (Tocris, 2939) and 100nM LDN193189 (Selleck Chemicals, S2618).
Growth protocol Mouse Pluripotent Stem Cell Culture: All mouse PSC lines; AV3, p2lac40, Sox17GFP, Pax9Venus, were maintained on mouse embryonic fibroblasts in KO DMEM (GIBCO, 10829) supplemented with 15% Hyclone FBS (Thermo Scientific, SH30070.03), 1% Glutamax (GIBCO, 35050079), 1% NEAA (Cellgro, 25-025-CI), 100µM β-mercaptoethanol (Invitrogen, 21985023), 1x103 units/ml ESGRO LIF (Millipore, ESG1107). Cells were fed daily and split every 2-3 days with 0.25% trypsin (GIBCO, 25200114).
Extracted molecule total RNA
Extraction protocol RNA was isolated using Trizol (Invitrogen, 15596-018) according to the manufacturer’s instructions.
Label biotin
Label protocol 500ng of total RNA was amplified and labeled using the Illumina Total Prep RNA Amplification Kit (Ambion, AMIL1791) according to the manufacturers’ instructions
 
Hybridization protocol Standard Illumina hybridization protocol
Scan protocol Standard Illumina scanning protocol
Description DE_Endoderm_3
replicate 3
Data processing Raw probe level intensity values were normalized using a variance stabilization approach by employing the R function vsn2 from the corresponding vsn package (Huber et al., 2002).
 
Submission date Nov 08, 2012
Last update date Apr 15, 2013
Contact name Michael Johannes Ziller
Organization name Max Planck Institute of Psychiatry
Department Translational Psychiatry
Lab Ziller lab
Street address Kraepelinstrasse 2-10
City Munich
ZIP/Postal code 80804
Country Germany
 
Platform ID GPL6885
Series (1)
GSE42139 Generation of organized anterior foregut epithelia from pluripotent stem cells using small molecules

Data table header descriptions
ID_REF
VALUE vsn normalized signal
DE_Endoderm_3.Detection Pval

Data table
ID_REF VALUE DE_Endoderm_3.Detection Pval
ILMN_2896528 11.80539192 0
ILMN_2721178 9.906097084 0
ILMN_3033922 9.783665001 0
ILMN_3092673 12.02910526 0
ILMN_2816356 4.546900822 0.1140351
ILMN_2808939 10.53761324 0
ILMN_2634564 9.467795027 0
ILMN_2737647 4.569988502 0.1090226
ILMN_2734484 9.722418147 0
ILMN_2952292 7.14192862 0
ILMN_2699078 4.532725006 0.1203008
ILMN_1213681 8.920626548 0
ILMN_2735413 3.411961906 0.6190476
ILMN_2735415 4.384480585 0.1716792
ILMN_2891688 9.560651078 0
ILMN_2637698 10.10148345 0
ILMN_2674228 9.588755989 0
ILMN_2601546 4.010536829 0.339599
ILMN_1230831 3.56952999 0.5526316
ILMN_2848071 4.575208805 0.1065163

Total number of rows: 25697

Table truncated, full table size 792 Kbytes.




Supplementary data files not provided
Raw data are available on Series record
Processed data included within Sample table

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