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Sample GSM606849 Query DataSets for GSM606849
Status Public on Jun 15, 2011
Title 4C WT mice Rad23a fetal liver replicate 2
Sample type genomic
 
Channel 1
Source name Rad23a 4C fetal liver, digested with HindIII and DpnII
Organism Mus musculus
Characteristics sample type: Rad23a 4C fetal liver, digested with HindIII and DpnII
genetic background: FVB
tissue: fetal liver
genotype: wild type
age: E14.5
Extracted molecule genomic DNA
Extraction protocol 4C was performed as described before in Simonis et al. 2006 Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat Genet. 38(11):1348-54
Label Cy3
Label protocol Details on the protocol can be found on http://www.nimblegen.com/technology/index.html
 
Channel 2
Source name WT genomic DNA fetal liver, digested with HindIII and DpnII
Organism Mus musculus
Characteristics sample type: WT genomic DNA fetal liver, digested with HindIII and DpnII
genetic background: FVB
tissue: fetal liver
genotype: wild type
age: E14.5
Extracted molecule genomic DNA
Extraction protocol 4C was performed as described before in Simonis et al. 2006 Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat Genet. 38(11):1348-54
Label Cy5
Label protocol Details on the protocol can be found on http://www.nimblegen.com/technology/index.html
 
 
Hybridization protocol Details on the protocol can be found on http://www.nimblegen.com/technology/index.html
Scan protocol Details on the protocol can be found on http://www.nimblegen.com/technology/index.html
Data processing Data were normalized using the 'lowess' method using standard settings (see Smyth & Speed, 2003, Methods 31, 265-273 (2003)
 
Submission date Oct 11, 2010
Last update date Jun 15, 2011
Contact name Elzo de Wit
Phone +31 30 2121 800
Organization name Hubrecht Institute
Street address Uppsalalaan 8
City Utrecht
ZIP/Postal code 3584 CT
Country Netherlands
 
Platform ID GPL4344
Series (1)
GSE24614 Variegated gene expression caused by cell-specific long-range DNA interactions

Data table header descriptions
ID_REF
CH1 Cy3 signal
CH2 Cy5 signal
VALUE lowess normalized Cy3/Cy5 signal

Data table
ID_REF CH1 CH2 VALUE
MMUS3C0000000002 1066.44 745.44 -0.137089493869875
MMUS3C0000000003 6514.78 801.56 3.17188656368188
MMUS3C0000000004 57535.11 45734.89 0.831218303372106
MMUS3C0000000005 1309.67 843.56 0.159576035194604
MMUS3C0000000006 1258.89 794.44 0.135905712976543
MMUS3C0000000007 922.22 683.78 -0.350284515907251
MMUS3C0000000008 1495.78 1259.56 0.0291444714917844
MMUS3C0000000009 1739.11 1374.44 0.222570459330979
MMUS3C0000000010 2346.56 2114.89 0.284580219216726
MMUS3C0000000012 3767.44 1254.11 1.70732360905210
MMUS3C0000000013 1060.33 602.56 0.0407328822261407
MMUS3C0000000014 1645.56 1937.67 -0.241910866231467
MMUS3C0000000015 2331.89 1309.22 0.810962030478118
MMUS3C0000000016 1302.56 839.22 0.15351488437893
MMUS3C0000000017 1792.89 771.89 0.854176403031121
MMUS3C0000000018 1425.89 731.67 0.457010487579586
MMUS3C0000000019 1842 858.56 0.80285516249102
MMUS3C0000000020 1334.56 1597 -0.42411031941305
MMUS3C0000000021 1588.44 1168.56 0.217474527290263
MMUS3C0000000022 2592.33 1215.44 1.08231347556245

Total number of rows: 385000

Table truncated, full table size 18969 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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