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Sample GSM519554 Query DataSets for GSM519554
Status Public on Jan 31, 2011
Title NP heterozygotes rep3
Sample type RNA
 
Source name Neuronal precursor cells, TDG heterozygotes, day 4
Organism Mus musculus
Characteristics differentiation stage: neuronal precursor
differentiation time days: 4
genotype: Tdg+/-
cell type: Neuronal precursor cells
Treatment protocol differentiation: embryoid body formation in absence of feeder cells and LIF, induction of differentiation with 5 µM all-trans retinoic acid and further growth in DMEM- F12 nutrient mixture (1:1) + 1x N2 supplement
Growth protocol ES cells: grown in DMEM, 15 % heat inactivated FCS, LIF (1,000 U/ml), 1x nonessential amino acids, 1 mM sodium pyruvate, 2 mM L-glutamine and 90 µM β-mercaptoethanol
Extracted molecule total RNA
Extraction protocol Total RNA was prepared using TRIZOL.
Label Cy3
Label protocol Starting with 500 ng / sample of total RNA, total RNAs was transcribed and labeled with Illumina(r) TotalPrep RNA Amplification Kit (Ambion). cRNA was quantified with QuantIT (Invitrogen) against ribosomal RNA standard (Invitrogen).
 
Hybridization protocol 1500 ng cRNA was hybridized on two Illumina MouseWG-6 v2 slides acording to the manufacturers protocol. Biological replicates were distributed among both slides.
Scan protocol Fluorescent signals were imaged by laser scanning using the Illumina iScan system.
Description n/a
Data processing The data was processed with Illumina genome studio software (gene expression module 1.0.6) with no background correction or normalization. VST (variance stabilization) transformation 'lumiT()', quantile normalization 'lumiN(, method = quantile)' and statistical analysis were performed with R (2.9.0) / Bioconductor using the package lumi (1.10.1) and libraries contained therein, in particular limma (2.16.4).
 
Submission date Mar 09, 2010
Last update date Jan 31, 2011
Contact name Fredy Siegrist
E-mail(s) fredy.siegrist@dkf.unibe.ch
Organization name University Hospital Bern
Department Department of Nephrology
Lab KKL D830
Street address Freiburgstrasse 15
City Bern
ZIP/Postal code 3010
Country Switzerland
 
Platform ID GPL6887
Series (1)
GSE20693 Effects of Tdg deficiency on overall transcription in mouse embryonic fibroblasts and during cell differentiation

Data table header descriptions
ID_REF
VALUE VST transformed - quantile normalized

Data table
ID_REF VALUE
ILMN_2659724 8.040469991
ILMN_2713160 8.103873132
ILMN_1219601 12.57413873
ILMN_1252621 10.83744789
ILMN_2574839 8.084486763
ILMN_3162407 10.13487349
ILMN_2514723 11.38968716
ILMN_2692952 10.85930658
ILMN_1257952 11.94386948
ILMN_1236559 8.04640153
ILMN_2910076 9.4000536
ILMN_1240428 8.126303982
ILMN_2459211 8.098454117
ILMN_2718462 8.180687781
ILMN_2882078 8.51456938
ILMN_2882079 8.227962723
ILMN_2570659 8.360953988
ILMN_2465544 8.553743937
ILMN_2724039 8.105161806
ILMN_2598594 10.05741943

Total number of rows: 45281

Table truncated, full table size 1100 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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