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Sample GSM2052431 Query DataSets for GSM2052431
Status Public on Apr 06, 2016
Title GB tissue 1
Sample type RNA
 
Source name GB tissue
Organism Mus musculus
Characteristics strain: C57BL/6
tissue/cell type: GB tissue
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 GT1
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 13.1043
10338002 6.80863
10338003 11.7241
10338004 10.0972
10338005 3.04654
10338006 3.31363
10338007 3.65607
10338008 4.49188
10338009 9.05758
10338010 3.08934
10338011 6.40759
10338012 3.19914
10338013 2.9412
10338014 2.98764
10338015 2.95851
10338016 8.24956
10338017 13.6422
10338018 7.30161
10338019 5.75236
10338020 8.82241

Total number of rows: 35556

Table truncated, full table size 586 Kbytes.




Supplementary file Size Download File type/resource
GSM2052431_Lugli_0913_TissueA_MoGene-1_0-st-v1_.CEL.gz 4.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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