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Sample GSM238448 Query DataSets for GSM238448
Status Public on Jul 07, 2008
Title Kms12 with IRF4 - slide 2 - repeat 2
Sample type genomic
 
Channel 1
Source name Kms12 with IRF4 antibody
Organism Homo sapiens
Characteristics Cell line: Kms12
Cell type: myeloma cell line
Treatment protocol Treatment type: compound
Agent: Anti-IRF4 Antibody
Treatment dose: 10 ug
Extracted molecule genomic DNA
Extraction protocol Genomic DNA Preparation Protocol
Other: Formaldehyde cross-linked, sonicated chromatin is prepared from cell lines Kms12 and Ly19 with chromatin immunoprecipitation protocol.
Label cy5
Label protocol Agilent Cy5 Labeling Protocol
Other: Whole genome amplified DNA is labeled using random primed Klenow enzyme based extension protocol according to Agilent's Mammalian ChIP-on-chip protocol v9.1.
 
Channel 2
Source name Kms12 Control
Organism Homo sapiens
Characteristics Cell line: Kms12
Cell type: myeloma cell line
Treatment protocol Treatment type: compound
Agent: Normal goat serum
Treatment dose: 10 ug
Extracted molecule genomic DNA
Extraction protocol Genomic DNA Preparation Protocol
Other: Formaldehyde cross-linked, sonicated chromatin is prepared from cell lines Kms12 and Ly19 with chromatin immunoprecipitation protocol.
Label cy3
Label protocol Agilent Cy3 Labeling Protocol
Other: Whole genome amplified DNA is labeled using random primed Klenow enzyme based extension protocol according to Agilent's Mammalian ChIP-on-chip protocol v9.1.
 
 
Hybridization protocol Agilent Hybridization Protocol
Other: Five micrograms of each Cy5 and Cy3 labeled DNA is hybridized to array for 40 hours at 65 degrees using Agilent ACGH/ChIp-chip hybridization and wash kits.
Scan protocol Agilent Scanning Protocol
Other: Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2505B, Agilent) using the default settings for 244k format two-color arrays.
Description No additional information.
Data processing Agilent Data Processing Protocol
Calculation Method: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software (Version 9.1.3.1). Spot values were normalized using the default normalization parameters.
 
Submission date Oct 18, 2007
Last update date Aug 14, 2011
Contact name Louis M. Staudt
E-mail(s) lstaudt@mail.nih.gov
Phone 301-402-1892
Organization name National Cancer Institute
Department Lymphoid Malignancies Branch
Lab Louis M Staudt
Street address 9000 Rockville Pike, Bldg 10, Rm 4N114
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL4125
Series (1)
GSE9367 IRF4 ChIP-on-chip for Myeloma Cell Lines

Data table header descriptions
ID_REF Agilent ID
VALUE normalized log10 ratio (Cy5/Cy3)
rDyeNormSignal Red Channel Signal with default normalization
gDyeNormSignal Green Channel Signal with default normalization

Data table
ID_REF VALUE rDyeNormSignal gDyeNormSignal
1 -0.2060115949 959.645 1542.13
2 -0.03143145163 252.687 271.653
3 -0.03383621401 248.81 268.97
4 -0.04502888788 628.629 697.306
5 -0.1317743363 489.654 663.23
6 -0.1086456721 901.944 1158.31
7 -0.1671832062 3684.38 5414.37
8 -0.02543324933 336.293 356.575
9 -0.06204271278 827.318 954.366
10 -0.1187578261 4989.73 6558.96
11 -0.1117483851 479.343 620.005
12 -0.1430943874 589.399 819.415
13 -0.1342850441 393.615 536.237
14 -0.06797268018 482.367 564.092
15 -0.08647658683 315.195 384.641
16 0.01199230891 357.379 347.646
17 -0.07550119534 422.077 502.219
18 -0.1003268585 297.332 374.601
19 -0.0505608994 598.408 672.293
20 -0.0551051162 1523.7 1729.83

Total number of rows: 243494

Table truncated, full table size 8691 Kbytes.




Supplementary file Size Download File type/resource
GSM238448.txt.gz 71.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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