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Sample GSM657933 Query DataSets for GSM657933
Status Public on Feb 25, 2017
Title Dnmt3ab KO Day0 (Total cDNA, 2nd biological replicate)
Sample type RNA
 
Channel 1
Source name Dnmt3ab KO Day0 (Total cDNA)
Organism Mus musculus
Characteristics cell type: Embryonic Stem Cell (ESC)
time: day 0
genotype: Dnmt3ab -/-
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. The genomic DNA isolated from CCE ES cell line was fragmented and used as Input DNA.
Label Cy5
Label protocol 1 µg ds-cDNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).
 
Channel 2
Source name J1 Day0 (Total cDNA)
Organism Mus musculus
Characteristics cell type: Embryonic Stem Cell (ESC)
time: day 0
genotype: Dnmt3ab -/-
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. The genomic DNA isolated from CCE ES cell line was fragmented and used as Input DNA.
Label Cy3
Label protocol 1 µg ds-cDNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).
 
 
Hybridization protocol 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. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html).
Scan protocol Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).
Description Dnmt3ab KO Day0 (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
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)

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

Data table
ID_REF green red VALUE
6379_0001_0001 472.06 90.25 -0.35
6379_0001_0007 415.69 89.44 -0.18
6379_0001_0019 519.06 138.94 0.13
6379_0001_0021 419.69 86 -0.25
6379_0001_0023 434.88 99.38 -0.09
6379_0001_0031 388.62 86.88 -0.13
6379_0001_0061 453.94 97.25 -0.19
6379_0001_0063 431.75 85.94 -0.29
6379_0001_0065 432.94 92.81 -0.19
6379_0001_0067 446.06 122.81 0.17
6379_0001_0077 435.25 89.25 -0.25
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 12815 Kbytes.




Supplementary file Size Download File type/resource
GSM657933_313215.txt.gz 4.0 Mb (ftp)(http) TXT
GSM657933_313215_532.pair.gz 5.5 Mb (ftp)(http) PAIR
GSM657933_313215_635.pair.gz 5.4 Mb (ftp)(http) PAIR
Processed data included within Sample table
Processed data provided as supplementary file

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