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Sample GSM657905 Query DataSets for GSM657905
Status Public on Feb 25, 2017
Title Fetal head dpc11.5 (Total cDNA)
Sample type mixed
Channel 1
Source name Fetal head dpc11.5 (Total cDNA)
Organism Mus musculus
Characteristics cell type: Fetal head
time: dpc 11.5
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.
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 dpc11.5 (Total cDNA)
Data processing Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.
Submission date Jan 19, 2011
Last update date Feb 25, 2017
Contact name Florian M Pauler
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)

Data table header descriptions
VALUE tukey normalized probe-level log2 ratio (Cy5/Cy3)

Data table
ID_REF green red VALUE
6379_0001_0001 324.11 230.33 0.27
6379_0001_0007 287.56 221.22 0.38
6379_0001_0019 2270.67 1272.56 -0.07
6379_0001_0021 745.56 227.44 -0.95
6379_0001_0023 305.67 258.67 0.52
6379_0001_0031 287.33 229.11 0.43
6379_0001_0061 303.33 200.11 0.16
6379_0001_0063 290.11 211 0.3
6379_0001_0065 290.67 195.89 0.19
6379_0001_0067 558.22 294.78 -0.16
6379_0001_0077 272.33 196.78 0.29
6379_0001_0085 null null null
6379_0001_0087 null null null
6379_0001_0089 null null null
6379_0001_0091 null null null
6379_0001_0093 null null null
6379_0001_0095 null null null
6379_0001_0097 null null null
6379_0001_0099 null null null
6379_0001_0101 null null null

Total number of rows: 392778

Table truncated, full table size 12908 Kbytes.

Supplementary file Size Download File type/resource
GSM657905_148958.txt.gz 4.0 Mb (ftp)(http) TXT
GSM657905_148958_532.pair.gz 5.4 Mb (ftp)(http) PAIR
GSM657905_148958_635.pair.gz 5.3 Mb (ftp)(http) PAIR
Processed data included within Sample table
Processed data provided as supplementary file

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