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Sample GSM66601 Query DataSets for GSM66601
Status Public on Sep 11, 2005
Title H33dN_3/TOTAL_4
Sample type genomic
 
Channel 1
Source name Chromatin affinity-purified DNA with tagged histone H3.3 core region from Drosophila S2 cells
Organism Drosophila melanogaster
Characteristics Chromatin affinity-purified DNA with tagged histone H3.3 core region from Drosophila S2 cells
Extracted molecule genomic DNA
Label Cy5
 
Channel 2
Source name Input DNA
Organism Drosophila melanogaster
Characteristics Input DNA
Extracted molecule genomic DNA
Label Cy3
 
 
Description Histones were identically tagged at their N-termini with biotin ligase recognition peptide (BLRP) (de Boer, E. et al. Proc Natl Acad Sci U S A 100, 7480-5 (2003), and Beckett, D. et al. Protein Sci 8, 921-9 (1999)) and expressed together with E. coli biotin ligase in Drosophila S2 cells. Nuclei were prepared as described (McKittrick, E., et al., Proc. Natl. Acad. Sci. USA 101, 1525-1530 (2004).), and treated with micrococcal nuclease (MNase) to digest chromatin to yield mostly mononucleosomes. Chromatin was extracted (input) using a modification of the procedure of Blower, M.D., et al. (Developmental Cell 2, 319-330 (2002)). Biotinylated histone-containing nucleosome particles (pull-down) were purified and DNA was extracted from both input and pull-down fraction for microarray analysis. DNA from input (3 ug) and pull-down (4 ug) was provided to NimbleGen Systems for differential labelling by random priming with Cy3- or Cy5 and hybridization to oligonucleotide arrays. For each experiment, input and pull-down channel signal intensities and scaled log2(ratios) were provided by NimbleGen Systems.
Data processing Log base 2 (PM_635/PM_532) ratios were bi-weight mean centered
 
Submission date Jul 28, 2005
Last update date Apr 11, 2012
Contact name Jorja Henikoff
E-mail(s) jorja@fhcrc.org
Phone 206-667-4850
Organization name Fred Hutchinson Cancer Research Center
Department Basic Sciences
Lab Henikoff
Street address 1100 Fairview AV N, A1-162
City Seattle
State/province WA
ZIP/Postal code 98109-1024
Country USA
 
Platform ID GPL2678
Series (1)
GSE3031 Genome-scale profiling of histone H3.3 replacement patterns in Drosophila S2 cells

Data table header descriptions
ID_REF NimbleGen PROBE_DESIGN_ID
PROBE_ID NimbleGen probe identifier
VALUE Log base 2 (PM_635/PM_532), bi-weight mean centered, for non-random oligos
PM_532 Cy3
PM_635 Cy5

Data table
ID_REF PROBE_ID VALUE PM_532 PM_635
1883_0001_0001 DMEL00P000244094 -0.50 12152.89 4555.33
1883_0001_0003 DMEL00P000141950 0.69 5492.11 4706.78
1883_0001_0005 DMEL00P000224218 -0.25 503.33 225.44
1883_0001_0007 DMEL00P000196684 -0.22 4935.56 2258.00
1883_0001_0009 DMEL00P000178692 -0.40 4431.00 1784.78
1883_0001_0011 DMEL00P000268603 1.27 17974.67 22946.33
1883_0001_0013 DMEL00P000272882 0.00 367.89 196.00
1883_0001_0015 DMEL00P000139092 0.10 13037.67 7404.44
1883_0001_0017 DMEL00P000198112 -0.23 1199.78 543.11
1883_0001_0019 DMEL00P000128833 -0.32 558.78 237.89
1883_0001_0021 DMEL00P000108410 1.77 6217.00 11275.56
1883_0001_0023 DMEL00P000075807 1.60 7700.78 12426.00
1883_0001_0025 DMEL00P000175495 -0.40 3364.11 1355.89
1883_0001_0027 DMEL00P000262384 -0.17 4014.89 1890.33
1883_0001_0029 DMEL00P000049933 0.19 1220.89 739.33
1883_0001_0031 DMEL00P000138543 0.76 11826.89 10604.22
1883_0001_0033 DMEL00P000033001 0.84 1473.00 1402.33
1883_0001_0035 DMEL00P000219905 -0.65 9578.44 3251.00
1883_0001_0037 DMEL00P000086137 1.54 2043.78 3157.33
1883_0001_0039 DMEL00P000112784 -0.14 5709.33 2757.33

Total number of rows: 388340

Table truncated, full table size 20060 Kbytes.




Supplementary file Size Download File type/resource
GSM66601.logratios.bedgraph.gz 2.3 Mb (ftp)(http) BEDGRAPH

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