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Sample GSM490204 Query DataSets for GSM490204
Status Public on Jun 14, 2010
Title ADF_K27_1_(294548-2)
Sample type genomic
 
Channel 1
Source name Amplified H3K27me3 ChIP.
Organism Arabidopsis thaliana
Characteristics tissue: root epidermis hair cell nuclei
cell line: ADF8p:NTF/ACT2p:BirA
Extracted molecule genomic DNA
Extraction protocol Amplification of ChIP DNA was done with Sigma WGA4 kit. Detailed protocol is located on the Series record.
Label Cy5
Label protocol Standard NimbleGen protocol using 5 hour labeling reaction rather than 2 hour reaction.
 
Channel 2
Source name Amplified H3 ChIP.
Organism Arabidopsis thaliana
Characteristics cell line: ADF8p:NTF/ACT2p:BirA
tissue: root epidermis hair cell nuclei
Extracted molecule genomic DNA
Extraction protocol Amplification of ChIP DNA was done with Sigma WGA4 kit. Detailed protocol is located on the Series record.
Label Cy3
Label protocol Standard NimbleGen protocol using 5 hour labeling reaction rather than 2 hour reaction.
 
 
Hybridization protocol Standard NimbleGen protocol.
Scan protocol Standard NimbleGen protocol.
Description Chromatin immunoprecipitation (ChIP) profiling of the H3K27me3 modification in INTACT-purified nuclei from Arabidopsis root hair cells.
Data processing Standard deviates of bi-weight mean adjusted log base 2 ratios of Cy5/Cy3 were computed.
 
Submission date Dec 24, 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 GPL7143
Series (1)
GSE19654 INTACT method for gene expression and chromatin profiling of individual cell types within a tissue

Data table header descriptions
ID_REF NimbleGen PROBE_ID
VALUE Standard deviate of log base 2 (Cy5/Cy3)

Data table
ID_REF VALUE
CHR1V01212004FS000000001 0.343
CHR1V01212004FS000000061 0.523
CHR1V01212004FS000000121 1.984
CHR1V01212004FS000000181 0.593
CHR1V01212004FS000000241 -0.667
CHR1V01212004FS000000301 0.963
CHR1V01212004FS000000361 -0.657
CHR1V01212004FS000000421 0.073
CHR1V01212004FS000000481 0.763
CHR1V01212004FS000000541 0.703
CHR1V01212004FS000000601 0.983
CHR1V01212004FS000000661 0.743
CHR1V01212004FS000000721 1.013
CHR1V01212004FS000000781 1.083
CHR1V01212004FS000000841 0.703
CHR1V01212004FS000000901 0.823
CHR1V01212004FS000000961 1.104
CHR1V01212004FS000001021 0.483
CHR1V01212004FS000001081 2.544
CHR1V01212004FS000001141 0.333

Total number of rows: 1982954

Table truncated, full table size 61082 Kbytes.




Supplementary file Size Download File type/resource
GSM490204_ADF_K27_1.bedgraph.gz 15.5 Mb (ftp)(http) BEDGRAPH
GSM490204_ADF_K27_1.gff.gz 22.1 Mb (ftp)(http) GFF
GSM490204_ADF_K27_1_532.pair.gz 33.3 Mb (ftp)(http) PAIR
GSM490204_ADF_K27_1_635.pair.gz 33.3 Mb (ftp)(http) PAIR
Processed data included within Sample table
Processed data provided as supplementary file

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