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Sample GSM66604 Query DataSets for GSM66604
Status Public on Sep 11, 2005
Title H33FL_1-2/H3_2-2
Sample type genomic
 
Channel 1
Source name Chromatin affinity-purified DNA with tagged histone H3.3 region from Drosophila S2 cells
Organism Drosophila melanogaster
Characteristics Chromatin affinity-purified DNA with tagged histone H3.3 from Drosophila S2 cells
Extracted molecule genomic DNA
Label Cy5
 
Channel 2
Source name Chromatin affinity-purified DNA with tagged histone H3 region from Drosophila S2 cells
Organism Drosophila melanogaster
Characteristics Chromatin affinity-purifed DNA with tagged histone H3 region from Drosophila S2 cells
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 -1.70 16425.22 4115.78
1883_0001_0003 DMEL00P000141950 0.62 2996.78 3749.67
1883_0001_0005 DMEL00P000224218 -1.17 1109.00 399.78
1883_0001_0007 DMEL00P000196684 -0.66 6164.44 3157.89
1883_0001_0009 DMEL00P000178692 -0.38 3803.33 2371.33
1883_0001_0011 DMEL00P000268603 -0.14 32371.00 23786.11
1883_0001_0013 DMEL00P000272882 0.20 1228.56 1147.67
1883_0001_0015 DMEL00P000139092 0.15 16244.00 14667.67
1883_0001_0017 DMEL00P000198112 -0.71 1954.33 972.11
1883_0001_0019 DMEL00P000128833 -0.41 3157.33 1926.89
1883_0001_0021 DMEL00P000108410 0.75 3358.33 4590.56
1883_0001_0023 DMEL00P000075807 0.61 6811.56 8467.67
1883_0001_0025 DMEL00P000175495 -0.42 2393.67 1450.00
1883_0001_0027 DMEL00P000262384 0.12 3746.11 3297.11
1883_0001_0029 DMEL00P000049933 0.25 2980.44 2874.22
1883_0001_0031 DMEL00P000138543 0.16 11762.22 10654.33
1883_0001_0033 DMEL00P000033001 -0.19 2234.33 1589.00
1883_0001_0035 DMEL00P000219905 -0.19 5638.11 4018.44
1883_0001_0037 DMEL00P000086137 0.90 8566.89 13015.22
1883_0001_0039 DMEL00P000112784 0.01 5586.33 4554.78

Total number of rows: 388340

Table truncated, full table size 20063 Kbytes.




Supplementary file Size Download File type/resource
GSM66604.logratios.bedgraph.gz 2.3 Mb (ftp)(http) BEDGRAPH

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