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Sample GSM2228446 Query DataSets for GSM2228446
Status Public on Jan 01, 2017
Title ESC H3K4me1-Rep2
Sample type genomic
 
Channel 1
Source name H3K4me1 ChIP DNA from 46c ESC
Organism Mus musculus
Characteristics cell type: 46c ESCs
chip antibody: H3K4me1
Growth protocol GMEM+ Supplement
Extracted molecule genomic DNA
Extraction protocol Nuclei from 3x10^6 mESCs or sorted Sox1+ve NPCs were prepared and resuspended in NB-R (85 mM NaCl, 5.5% Sucrose, 10mM TrisHCl pH 7.5, 3 mM MgCl2, 1.5 mM CaCl2, 0.2 mM PMSF, 1 mM DTT), Micrococcal nuclease (MNase) digestion and native ChIP were performed as previously described (Eskeland et al. 2010, Pradeepa et al.2012) Antibodies used for ChIP were; H3K4me1 (Abcam ab8895) and H3K27ac (Millipore 07-360).
Label Cy3
Label protocol Ten nanograms (optimal) of input or ChIP DNA were amplified using the WGA2 whole genome amplification kit (Sigma). Amplified material was labelled with Cy3 or Cy5 by random priming according to the NimbleGen ChIP-chip protocol (Roche). In total, 2 or 3 biological replicates with dye swaps were hybridized for 20 h and washed according to manufacturer´s protocol. A custom 3x720K mouse tiling array (NimbleGen, Roche) containing 179,493 unique probes from different genomic regions, with each probe represented by 4 replicates was used.
 
Channel 2
Source name Input DNA from 46c ESCs
Organism Mus musculus
Characteristics cell type: 46c ESCs
control type: input DNA
Growth protocol GMEM+ Supplement
Extracted molecule genomic DNA
Extraction protocol Nuclei from 3x10^6 mESCs or sorted Sox1+ve NPCs were prepared and resuspended in NB-R (85 mM NaCl, 5.5% Sucrose, 10mM TrisHCl pH 7.5, 3 mM MgCl2, 1.5 mM CaCl2, 0.2 mM PMSF, 1 mM DTT), Micrococcal nuclease (MNase) digestion and native ChIP were performed as previously described (Eskeland et al. 2010, Pradeepa et al.2012) Antibodies used for ChIP were; H3K4me1 (Abcam ab8895) and H3K27ac (Millipore 07-360).
Label Cy5
Label protocol Ten nanograms (optimal) of input or ChIP DNA were amplified using the WGA2 whole genome amplification kit (Sigma). Amplified material was labelled with Cy3 or Cy5 by random priming according to the NimbleGen ChIP-chip protocol (Roche). In total, 2 or 3 biological replicates with dye swaps were hybridized for 20 h and washed according to manufacturer´s protocol. A custom 3x720K mouse tiling array (NimbleGen, Roche) containing 179,493 unique probes from different genomic regions, with each probe represented by 4 replicates was used.
 
 
Hybridization protocol The labeled ChIP DNA was hybridized for 16-18 h at 42C, and then washed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)
Scan protocol Arrays were scanned on a NimbleGen MS 200 Microarray scanner (Roche) using 100% laser power and 2μm resolution.
Description ChIP-chip ESCs H3K4me1
Data processing Raw signal intensities were quantified from TIFF images using MS 200 Data Collection software. Microarray data were analysed in R using the bioconductor packages Beadarray and Limma according to the Epigenesys NimbleGen ChIP-on-chip protocol 43. Replicate probe values were collapsed to the arithmetic mean prior to generating log2 (ChIP/Input) ratios.
 
Submission date Jul 07, 2016
Last update date Jan 01, 2017
Contact name Rob S Illingworth
E-mail(s) robert.illingworth@ed.ac.uk
Phone 01316519640
Organization name The University of Edinburgh
Department Centre for regenerative Medicine
Lab Illingworth
Street address Centre for Regenerative Medicine
City Edinburgh
State/province Midlothian
ZIP/Postal code EH16 4UU
Country United Kingdom
 
Platform ID GPL22129
Series (1)
GSE84168 Identification of a novel long-range enhancer driving Sonic Hedgehog expression in neural progenitor cells

Data table header descriptions
ID_REF
VALUE log2 (ChIP/Input)

Data table
ID_REF VALUE
CHR10FS126746006 0.76
CHR10FS126746061 0.88
CHR10FS126746111 0.89
CHR10FS126746171 0.51
CHR10FS126746246 0.28
CHR10FS126746371 0.78
CHR10FS126746426 0.65
CHR10FS126746526 0.07
CHR10FS126746576 0.63
CHR10FS126746631 1.8
CHR10FS126746681 0.9
CHR10FS126746761 0.33
CHR10FS126746906 0.8
CHR10FS126746956 1.5
CHR10FS126747011 1.18
CHR10FS126747066 0.47
CHR10FS126747121 1.55
CHR10FS126747176 1.54
CHR10FS126747231 0.36
CHR10FS126747281 0.75

Total number of rows: 354999

Table truncated, full table size 7744 Kbytes.




Supplementary file Size Download File type/resource
GSM2228446_527916A01_2012-02-17_14-59_Area1_532.pair.gz 11.9 Mb (ftp)(http) PAIR
GSM2228446_527916A01_2012-02-17_14-59_Area1_635.pair.gz 11.9 Mb (ftp)(http) PAIR
GSM2228446_esc_h3k4me1_2-raw.bedGraph.gz 2.6 Mb (ftp)(http) BEDGRAPH
Processed data included within Sample table
Processed data provided as supplementary file

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