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Sample GSM1226201 Query DataSets for GSM1226201
Status Public on Dec 31, 2013
Title BRAF(V600K)-G-rep1
Sample type RNA
 
Source name Lgr5-EGFP-positive crypt cells, BRAF(V600K) transgene negative
Organism Mus musculus
Characteristics cell type: Lgr5-EGFP-positive crypt cells
transgene: BRAF(V600K) transgene negative
genetic background: B6/129S6 mixed
organ: duodenum
Treatment protocol Cells were gated into different fractions, by high versus low green fluorescence (Lgr5-EGFP stem cell specific reporter) and high versus low red fluorescence (inducible TdTomato-BRAF(V600K) or TdTomato-luciferase control transgene). Resulting cell populations are labelled RG, R, G and NEG.
Growth protocol Mice were housed at a 12h/12h light/dark cycle and fed ad libitum. Transgenes were induced by doxycycline (4mg/ml) treatment provided in a 1% sucrose solution in the drinking water of transgenic mice. Single cell suspensions were isolated from intestinal crypts of mice aged 8-12weeks.
Extracted molecule total RNA
Extraction protocol Cells were sorted into Qiagen buffer RLT+1%beta-Mercaptoethanol, and RNA was extracted using RNeasy Micro columns
Label Biotin-Cy3
Label protocol Probes were labelled using the NuGen Procedure (at Company AROS, Aarhus, DK)
 
Hybridization protocol Arrays were hybridized using the NuGen Procedure (at Company AROS, Aarhus, DK)
Scan protocol Standard Illumina scanning protocol
Description BRAF Mouse 1
Data processing Illumina Genome Studio GX 1.9.0, Quantile Normalisation
 
Submission date Sep 06, 2013
Last update date Aug 20, 2014
Contact name Markus Morkel
E-mail(s) markus.morkel@charite.de
Organization name Charité - Universitätsmedizin Berlin
Department Dept. of Pathology
Lab Laboratory of Molecular Tumour Pathology
Street address Charitéplatz 1
City Berlin
ZIP/Postal code 10117
Country Germany
 
Platform ID GPL6885
Series (1)
GSE50678 Transcriptional Response to transgenic BRAF(V600K) in the intestinal epithelium

Data table header descriptions
ID_REF
VALUE quantile normalized, no background substraction
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_2896528 546.8 0
ILMN_2721178 270.4 0
ILMN_3033922 254.9 0
ILMN_3092673 1161.7 0
ILMN_2816356 181.6 0.00376
ILMN_2808939 1182.1 0
ILMN_2634564 1546.9 0
ILMN_2737647 93.1 0.25439
ILMN_2734484 539.8 0
ILMN_2952292 193.7 0.00251
ILMN_2699078 311.9 0
ILMN_1213681 340.4 0
ILMN_2735413 91.1 0.29323
ILMN_2735415 78.6 0.64912
ILMN_2891688 851.7 0
ILMN_2637698 262.6 0
ILMN_2674228 147.2 0.0213
ILMN_2601546 86.8 0.37469
ILMN_1230831 123.5 0.06642
ILMN_2848071 145.6 0.02381

Total number of rows: 25697

Table truncated, full table size 613 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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