|
Status |
Public on Feb 25, 2017 |
Title |
Fetal head dpc14.5 (Total cRNA, 1st biological replicate) |
Sample type |
mixed |
|
|
Channel 1 |
Source name |
Fetal head dpc14.5 (Total RNA)
|
Organism |
Mus musculus |
Characteristics |
cell type: Fetal head time: dpc14.5 genotype: wt
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted from different tissues or cells. After the treatment of DNase I, total RNA was reverse transcribed, and synthesized to double-stranded cDNA.
|
Label |
Cy5
|
Label protocol |
Labelling was performed by imaGenes GmbH (Berlin Germany). In brief: 1 µg ds-cDNA was directly labeled by Klenow (New England Biolabs) random priming with Cy5 nonamers.
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|
|
Channel 2 |
Source name |
Input (CCE Day0, sonicated genomic DNA)
|
Organism |
Mus musculus |
Characteristics |
cell type: Embryonic Stem Cell (ESC) time: day 0 genotype: CCE
|
Growth protocol |
ESCs were cultured in Hepes-buffered DMEM, supplemented with Leukaemia Inhibitory Factor (LIF), 15% FCS, 50µg/ml Gentamicin, 1× MEM, 1mM NaPyruvate, 2mM L-Glutamin and 2mM β-mercaptoethanol, in 5% CO2 atmosphere at 37°C. For feeder independent ES cell culture, all dishes and flasks were gelatinized with 0.2% Gelatin solution (diluted in DPBS) at RT for 20min before use.
|
Extracted molecule |
genomic DNA |
Extraction protocol |
The genomic DNA isolated from CCE ES cell line was fragmented and used as Input DNA.
|
Label |
Cy3
|
Label protocol |
Labelling was performed by imaGenes GmbH (Berlin Germany). In brief: 1 µg ds-cDNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers.
|
|
|
|
Hybridization protocol |
Hybridisation was performed by imaGenes GmbH (Berlin Germany). In brief: The labeled ds-cDNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC.
|
Scan protocol |
Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol by imaGenes GmbH (Berlin Germany).
|
Description |
Fetal head dpc14.5 (Total RNA)
|
Data processing |
Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.
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|
|
Submission date |
Jan 19, 2011 |
Last update date |
Feb 25, 2017 |
Contact name |
Florian M Pauler |
E-mail(s) |
florian.pauler@ist.ac.at
|
Phone |
+43 2243 9000-7434
|
Organization name |
IST Austria
|
Lab |
Simon Hippenmeyer
|
Street address |
Am Campus 1
|
City |
Klosterneuburg |
ZIP/Postal code |
3400 |
Country |
Austria |
|
|
Platform ID |
GPL11618 |
Series (2) |
GSE26718 |
Macro ncRNAs are abundant in imprinted regions and directly regulated by DNA methylation [tiling array] |
GSE75454 |
Transcript identification and quantification on Mouse Imprinted Region Tiling Array (MIRTA) |
|