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Sample GSM175625 Query DataSets for GSM175625
Status Public on Jul 28, 2007
Title kidney H3K4me3 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 1 of 4
Sample type genomic
 
Channel 1
Source name Chromatin immunoprecipitated DNA from kidney cells using H3K4me3 antibody
Organism Mus musculus
Characteristics cells: kidney immunoprecipitated chromatin
Extracted molecule genomic DNA
Extraction protocol immunoprecipitated chromatin
Label Cy5
Label protocol Cy5
 
Channel 2
Source name Input Chromatin kidney cells.
Organism Mus musculus
Characteristics cells: kidney input chromatin
Extracted molecule genomic DNA
Extraction protocol input chromatin
Label Cy3
Label protocol Cy3
 
 
Hybridization protocol NimbleGen hybridization protocol
Scan protocol NimbleGen scan protocol
Description Chromatin immunoprecipitation was performed using antibodies against H3K4me3 and formaldehyde crosslinked chromatin from kidney cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI33 build of the mouse genome (mm5) that contains non-overlapping 50-mer oligonucleotides, positioned at every 100 basepairs (bp)
Data processing Condensed array sets (1-4) for all tissues were either loess normalized or median normalized using the R package limma with the normalization using the RANDOM_GC probes.
 
Submission date Mar 15, 2007
Last update date May 03, 2007
Contact name Bing Ren
E-mail(s) biren@ucsd.edu
Organization name Ludwig Institute for Cancer Research
Department Department of Cellular and Molecular Medicine
Lab Laboratory of Gene Regulation
Street address 9500 Gilman Drive
City La Jolla
State/province CA
ZIP/Postal code 92093-0653
Country USA
 
Platform ID GPL4931
Series (1)
GSE7688 Genome-wide mapping and analysis of active promoters in mouse ES cells and adult organs

Data table header descriptions
ID_REF PROBE_DESIGN_ID
VALUE log2R normalized
INT_635 Cy5 intensity raw from pair file
INT_532 Cy3 intensity raw from pair file

Data table
ID_REF VALUE INT_635 INT_532
2249_0006_0003 0 7316.22 26523.45
2249_0008_0003 0 7627.89 25034.45
2249_0010_0003 0 7312.78 25304.45
2249_0012_0003 0 8093.22 26819.67
2249_0007_0004 0 6450.67 53887.45
2249_0009_0004 0 6628.33 49881.11
2249_0011_0004 0 6192.00 46243.45
2249_0013_0004 0 6182.00 43626.22
2249_0006_0005 0 8311.22 25806.45
2249_0008_0005 0 7046.78 24552.33
2249_0010_0005 0 7530.67 25430.11
2249_0012_0005 0 6771.00 54575.78
2249_0007_0006 0 6462.00 56567.45
2249_0009_0006 0 6168.11 53096.33
2249_0011_0006 0 7826.78 25312.45
2249_0013_0006 0 6169.00 46092.55
2249_0006_0007 0 7423.89 26002.55
2249_0008_0007 0 8179.11 25472.22
2249_0010_0007 0 7823.89 25919.22
2249_0012_0007 0 8448.00 27136.78

Total number of rows: 390611

Table truncated, full table size 13985 Kbytes.




Supplementary file Size Download File type/resource
GSM175625_532.pair.gz 7.4 Mb (ftp)(http) PAIR
GSM175625_635.pair.gz 7.3 Mb (ftp)(http) PAIR

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