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Sample GSM2052419 Query DataSets for GSM2052419
Status Public on Apr 06, 2016
Title differentiated gallbladder organoid 1
Sample type RNA
 
Source name differentiated gallbladder organoid
Organism Mus musculus
Characteristics strain: C57BL/6
tissue/cell type: differentiated gallbladder organoid
Treatment protocol Differentiated gallbladder organoids were obtained by culturing the organoids in media lacking R-spondin 1, noggin and nicotinamide for two weeks.
Growth protocol Organoids were cultured in Matrigel with tissue culture media based on AdDMEM/F12 (Life Technologies) and supplemented with B27, N2 (Life Technologies) and 1.25 uM N-Acetylcysteine (Sigma-Aldrich). The following growth factors were also added: 50 ng/mL murine recombinant EGF (Life Technologies), 50 ng/mL murine recombinant FGF10 (R&D system), 10 mM nicotinamide (Sigma-Aldrich), 50 ng/mL murine recombinant HGF (Peprotech) and R-spondin 1 and noggin home-made conditioned media (prepared as in Sato et al., Nature 459: 262-265, 2009).
Extracted molecule total RNA
Extraction protocol RNA was extracted from liver, gallbladder or small intestine tissues, and liver, gallbladder or small intestine organoids using the RNeasy Mini RNA Extraction Kit (Qiagen).
Label biotin
Label protocol 5.5 ug of ds cDNA were fragmented and labeled using the GeneChip WT DNA terminal labeling kit.
 
Hybridization protocol Biotinylated cRNA was fragmented and hybridized to GeneChip Mouse Gene 1.0 ST Arrays (Affymetrix) following the standard protocol of the manufacturer.
Scan protocol Standard Affymetrix.
Description D1
Data processing RMA Probes to Import: Interrogating Probes, Probe filtering: skip,Algorithm: RMA,Background Correction: RMA Background Correction,Normalization: Quantile Normalization,Log Probes using Base: 2,Probeset Summarization: Median Polish
 
Submission date Feb 02, 2016
Last update date Apr 06, 2016
Contact name Thanos Halazonetis
E-mail(s) [email protected]
Organization name University of Geneva
Department IDepartment of Molecular Biology
Lab Thanos Halazonetis
Street address Sciences III, 30, quai Ernest-Ansermet
City Geneva
State/province GE
ZIP/Postal code 1211
Country Switzerland
 
Platform ID GPL6246
Series (1)
GSE77461 R-spondin 1 and noggin facilitate expansion of resident stem cells from non-damaged gallbladders.

Data table header descriptions
ID_REF
VALUE Log2 normalized

Data table
ID_REF VALUE
10338001 12.2705
10338002 7.65503
10338003 10.4833
10338004 9.13995
10338005 3.08773
10338006 3.48252
10338007 4.0913
10338008 5.22897
10338009 9.24881
10338010 3.13644
10338011 7.19017
10338012 3.30127
10338013 2.92236
10338014 3.00481
10338015 2.92054
10338016 8.76581
10338017 12.861
10338018 8.07041
10338019 6.69316
10338020 9.1749

Total number of rows: 35556

Table truncated, full table size 586 Kbytes.




Supplementary file Size Download File type/resource
GSM2052419_Kamileri_Lugli_121115_NR1_MoGene-1_0-st-v1_.CEL.gz 4.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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