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Sample GSM581036 Query DataSets for GSM581036
Status Public on Feb 08, 2011
Title ZF4_H3K27me3_Repl2
Sample type genomic
 
Channel 1
Source name H3K27me3 ChIP DNA
Organism Danio rerio
Characteristics cell line: ZF4
source: American Type Culture Collection
developmental stage: Embryo
chip antibody: anti-H3K27me3 from Millipore (cat# 07-449)
Growth protocol Cell grown under standard condition as per Driever and Rangini, 1993 In vitro Cell Dev Biol.Anim 294, 749
Extracted molecule genomic DNA
Extraction protocol Histone ChIPs were done as described (Dahl, Collas, 2007) using 0.5 A260 units chromatin per ChIP. In short, cells were cross-linked in suspension with 1% formaldehyde for 8 min and quenched with glycine. Lysis buffer was added to ~120 µl and samples incubated for 5 min on ice. Cells were sonicated on ice using a Bioruptor (Diagenode) to produce fragments of ~400 bp. The lysate was centrifuged, the supernatant collected, chromatin diluted to 0.5 A260 units and 100 µl was incubated with 2.4 μg antibody coupled to Dynabeads Protein A (Invitrogen) for 2 h at 4oC. ChIP material was washed as described [46]. Elution buffer containing 1 % SDS and 50 µg/ ml Proteinase K was added and samples incubated for 2 h at 68oC on a Thermomixer (Eppendorf); after a second extraction both supernatants were pooled. ChIP DNA was purified by phenol-chloroform isoamylalcohol extraction, ethanol-precipitated and dissolved in 50 μl TE buffer. 5 µg (10 µl) RNase A (Roche) was added before ChIP DNA elution. ChIP DNA samples were dissolved in 16 μl MilliQ water. Input DNA (channel 2) was purified by phenol-chloroform isoamylalcohol extraction and RNAse-treated as above.
Label Cy5
Label protocol Labeling done by Nimblegen as per normal service protocol
 
Channel 2
Source name Input DNA from ZF4 cells
Organism Danio rerio
Characteristics cell line: ZF4
source: American Type Culture Collection
developmental stage: Embryo
Growth protocol Cell grown under standard condition as per Driever and Rangini, 1993 In vitro Cell Dev Biol.Anim 294, 749
Extracted molecule genomic DNA
Extraction protocol Histone ChIPs were done as described (Dahl, Collas, 2007) using 0.5 A260 units chromatin per ChIP. In short, cells were cross-linked in suspension with 1% formaldehyde for 8 min and quenched with glycine. Lysis buffer was added to ~120 µl and samples incubated for 5 min on ice. Cells were sonicated on ice using a Bioruptor (Diagenode) to produce fragments of ~400 bp. The lysate was centrifuged, the supernatant collected, chromatin diluted to 0.5 A260 units and 100 µl was incubated with 2.4 μg antibody coupled to Dynabeads Protein A (Invitrogen) for 2 h at 4oC. ChIP material was washed as described [46]. Elution buffer containing 1 % SDS and 50 µg/ ml Proteinase K was added and samples incubated for 2 h at 68oC on a Thermomixer (Eppendorf); after a second extraction both supernatants were pooled. ChIP DNA was purified by phenol-chloroform isoamylalcohol extraction, ethanol-precipitated and dissolved in 50 μl TE buffer. 5 µg (10 µl) RNase A (Roche) was added before ChIP DNA elution. ChIP DNA samples were dissolved in 16 μl MilliQ water. Input DNA (channel 2) was purified by phenol-chloroform isoamylalcohol extraction and RNAse-treated as above.
Label Cy3
Label protocol Labeling done by Nimblegen as per normal service protocol
 
 
Hybridization protocol Hybridization done by Nimblegen as per normal service protocol
Scan protocol Scanning done by Nimblegen as per normal service protocol
Data processing log2 (ChIP/Input) with biweight mean of values subtracted
 
Submission date Aug 18, 2010
Last update date Feb 09, 2011
Contact name Philippe Collas
Organization name University of Oslo
Department Institute of Basic Medical Sciences
Street address PO Box 1112 Blindern
City Oslo
ZIP/Postal code 0317
Country Norway
 
Platform ID GPL10835
Series (2)
GSE23691 Mapping of H3K4 and H3K27 trimethylation in zebrafish cells (ChIP-chip)
GSE23872 Mapping of H3K4 and H3K27 trimethylation in zebrafish cells

Data table header descriptions
ID_REF
VALUE log2(Cy5/Cy3) – biweight_mean

Data table
ID_REF VALUE
CHR01FS000015029 2.19
CHR01FS000015119 2.29
CHR01FS000015501 1.99
CHR01FS000015597 2.21
CHR01FS000015679 2.11
CHR01FS000015755 2.33
CHR01FS000015943 2.42
CHR01FS000016141 0.85
CHR01FS000016227 0.85
CHR01FS000016483 0.97
CHR01FS000016567 2.47
CHR01FS000016767 2.37
CHR01FS000016857 2.43
CHR01FS000016935 1.83
CHR01FS000017013 1.09
CHR01FS000017113 1.91
CHR01FS000017215 2.13
CHR01FS000017283 2.46
CHR01FS000017385 2.71
CHR01FS000017485 2.37

Total number of rows: 2168225

Table truncated, full table size 47615 Kbytes.




Supplementary file Size Download File type/resource
GSM581036_ZF4_H3K27me3_2_532.pair.gz 34.5 Mb (ftp)(http) PAIR
GSM581036_ZF4_H3K27me3_2_635.pair.gz 34.0 Mb (ftp)(http) PAIR
Processed data included within Sample table

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