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Sample GSM468560 Query DataSets for GSM468560
Status Public on Dec 08, 2009
Title H3.3_350mM_salt_fraction_(SOH12)
Sample type genomic
 
Channel 1
Source name H3.3 DNA pull-down
Organism Caenorhabditis elegans
Characteristics age: embryos
strain: N2 (Bristol)
Extracted molecule genomic DNA
Extraction protocol H3.3 Streptavidin pulldown from 350 mM salt soluble fraction compared to the 350 mM salt soluble fraction. Detailed protocol at http://nettie.fhcrc.org/modencode/protocols/Worm_Protocol.doc
Label Cy3
Label protocol Standard NimbleGen protocol.
 
Channel 2
Source name H3.3 DNA input
Organism Caenorhabditis elegans
Characteristics age: embryos
strain: N2 (Bristol)
Extracted molecule genomic DNA
Extraction protocol Detailed protocol at http://nettie.fhcrc.org/modencode/protocols/Worm_Protocol.doc
Label Cy5
Label protocol Standard NimbleGen protocol.
 
 
Hybridization protocol Standard NimbleGen protocol.
Scan protocol Standard NimbleGen protocol.
Description 350mM NaCl-extracted chromatin
Data processing Adjusted log base 2 ratios of Cy3/Cy5 were computed using the method of Peng, et al (BMC Bioinformatics, 2007,8:219,PMID 17592629). The adjusted log ratios were converted to standard deviates by subtracting their mean and dividing by their standard deviation. (NOTE: the supplementary files have the adjusted log ratios, not their standard deviates.)
 
Submission date Nov 05, 2009
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 GPL7098
Series (1)
GSE18898 A native chromatin purification system for epigenomic profiling in C. elegans

Data table header descriptions
ID_REF NimbleGen PROBE_ID
VALUE Log base 2 (Cy3/Cy5), Peng-adjusted standard deviates

Data table
ID_REF VALUE
IFS000000001 -0.312
IFS000000047 -0.459
IFS000000093 -0.073
IFS000000139 -0.197
IFS000000185 -0.656
IFS000000231 -0.341
IFS000000277 0.088
IFS000000323 0.203
IFS000000369 -0.139
IFS000000415 2.231
IFS000000461 2.083
IFS000000507 1.829
IFS000000553 2.6
IFS000000599 1.207
IFS000000645 0.801
IFS000000691 0.751
IFS000000737 1.323
IFS000000783 1.536
IFS000000829 0.094
IFS000000875 -2.607

Total number of rows: 2143307

Table truncated, full table size 41895 Kbytes.




Supplementary file Size Download File type/resource
GSM468560_SOH12_532.pair.gz 34.7 Mb (ftp)(http) PAIR
GSM468560_SOH12_635.pair.gz 34.7 Mb (ftp)(http) PAIR
GSM468560_SOH12_WS190.bedgraph.gz 30.9 Mb (ftp)(http) BEDGRAPH
GSM468560_SOH12_WS190.gff.gz 40.0 Mb (ftp)(http) GFF
Processed data included within Sample table

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