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Status |
Public on Jan 31, 2011 |
Title |
ES knockout rep2 |
Sample type |
RNA |
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Source name |
Embryonic stem cells, TDG knock-out
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Organism |
Mus musculus |
Characteristics |
differentiation stage: embryonal stem differentiation time days: 0 genotype: Tdg-/- cell type: Embryonic stem cells
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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
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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
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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).
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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.
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Scan protocol |
Fluorescent signals were imaged by laser scanning using the Illumina iScan system.
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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).
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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 |
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