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Sample GSM490206 Query DataSets for GSM490206
Status Public on Jun 14, 2010
Title ADF_K4_1_(294553-2)
Sample type genomic
 
Channel 1
Source name Amplified H3K4me3 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 H3K4me3 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 0.4
CHR1V01212004FS000000061 -0.379
CHR1V01212004FS000000121 -0.521
CHR1V01212004FS000000181 0.203
CHR1V01212004FS000000241 -0.653
CHR1V01212004FS000000301 -0.895
CHR1V01212004FS000000361 -0.543
CHR1V01212004FS000000421 -0.993
CHR1V01212004FS000000481 -1.125
CHR1V01212004FS000000541 -1.388
CHR1V01212004FS000000601 -0.653
CHR1V01212004FS000000661 -1.059
CHR1V01212004FS000000721 -0.51
CHR1V01212004FS000000781 -0.576
CHR1V01212004FS000000841 -0.719
CHR1V01212004FS000000901 -0.423
CHR1V01212004FS000000961 1.366
CHR1V01212004FS000001021 -0.401
CHR1V01212004FS000001081 1.783
CHR1V01212004FS000001141 -0.126

Total number of rows: 1982954

Table truncated, full table size 60911 Kbytes.




Supplementary file Size Download File type/resource
GSM490206_ADF_K4_1.bedgraph.gz 15.4 Mb (ftp)(http) BEDGRAPH
GSM490206_ADF_K4_1.gff.gz 21.8 Mb (ftp)(http) GFF
GSM490206_ADF_K4_1_532.pair.gz 33.2 Mb (ftp)(http) PAIR
GSM490206_ADF_K4_1_635.pair.gz 33.1 Mb (ftp)(http) PAIR
Processed data included within Sample table
Processed data provided as supplementary file

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