NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM601452 Query DataSets for GSM601452
Status Public on Feb 15, 2011
Title BCL6 ChIP-chip in BV173 cells + 10┬ÁM STI571 (24h) replicate 1
Sample type genomic
 
Channel 1
Source name genomic DNA [input]
Organism Homo sapiens
Characteristics cell type: Ph+ ALL cell line BV-173
agent: STI571 (10uM)
chip antibody: none, input DNA
Extracted molecule genomic DNA
Extraction protocol sonicated genomic DNA, then purify by qiagen column
Label Cy3
Label protocol described in www.nimblegen.com
 
Channel 2
Source name BCL6 ChIP DNA from ph+ ALL cell line [IP]
Organism Homo sapiens
Characteristics cell type: Ph+ ALL cell line BV-173
agent: STI571 (10uM)
chip antibody: BCL6
chip antibody vendor: Santa Cruz Biotechnology
chip antibody lot #: I2607
chip antibody catalog #: sc-858
Extracted molecule genomic DNA
Extraction protocol chromatinIP products which are genomic regions bound by BCL6, then purify by qiagen column.
Label Cy5
Label protocol described in www.nimblegen.com
 
 
Hybridization protocol Standard Nimblegen protocol.
Scan protocol Standard Nimblegen protocol.
Description BV173_S_r1_WC9
BCL6 ChIP-chip in BV173 cells treated with 10uM STI571 (24h) replicate 1
chip-on-chip is performing in three Ph+ ALL cell lines (BV-173, NALM-1 and TOM-1) in duplicate by BCL6 antibody
Data processing Take all the probes in the promoter region and perform Log2 transformion of IP/INPUT(Cy5/Cy3). Then use the maximal summary of three connected probes as the bound intensity of the promoter.
The analysis method (script) was published in Ci et al. Blood. 2009 May 28;113(22):5536-48. PMID: 19307668.
 
Submission date Sep 28, 2010
Last update date Feb 15, 2011
Contact name Huimin Geng
E-mail(s) huimin.geng@ucsf.edu
Organization name UCSF
Department Department of Laboratory Medicine
Street address 513 Parnassus Ave., MSB S-1480
City San Francisco
State/province CA
ZIP/Postal code 94143
Country USA
 
Platform ID GPL8275
Series (2)
GSE24404 Recruitment of BCL6 to target genes in Philadelphia chromosome positive acute lymphoblastic leukemia
GSE24426 BCL6 enables leukemia cells to cope with inhibition of oncogenic tyrosine kinases

Data table header descriptions
ID_REF
VALUE Log2 transformed IP/INPUT(CY5/CY3)

Data table
ID_REF VALUE
HSAP0406S00000003 -1.158460216
HSAP0406S00000005 1.344261061
HSAP0406S00000008 -0.588195143
HSAP0406S00000009 -0.182736212
HSAP0406S00000010 -0.536187488
HSAP0406S00000011 -0.523986116
HSAP0406S00000012 -0.445182414
HSAP0406S00000013 -0.565631578
HSAP0406S00000014 -0.364576476
HSAP0406S00000015 -0.026518668
HSAP0406S00000016 -0.500126061
HSAP0406S00000017 -0.971920547
HSAP0406S00000018 0.847850289
HSAP0406S00000019 -0.076119666
HSAP0406S00000020 -0.752753906
HSAP0406S00000022 -1.207899219
HSAP0406S00000025 -0.647589253
HSAP0406S00000027 -0.825324153
HSAP0406S00000029 -1.009538006
HSAP0406S00000031 -1.050913361

Total number of rows: 24134

Table truncated, full table size 717 Kbytes.




Supplementary file Size Download File type/resource
GSM601452_268745-WC-9-081222_532.pair.gz 6.2 Mb (ftp)(http) PAIR
GSM601452_268745-WC-9-081222_635.pair.gz 6.2 Mb (ftp)(http) PAIR
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap