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Sample GSM601456 Query DataSets for GSM601456
Status Public on Feb 15, 2011
Title BCL6 ChIP-chip in NALM1 cells + 10┬ÁM STI571 (24h) replicate 2
Sample type genomic
 
Channel 1
Source name genomic DNA [input]
Organism Homo sapiens
Characteristics cell type: Ph+ ALL cell line NALM-1
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 NALM-1
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 NALM1_S_r2_WC13
BCL6 ChIP-chip in NALM1 cells treated with 10uM STI571 (24h) replicate 2
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 -2.270794094
HSAP0406S00000005 1.688235293
HSAP0406S00000008 -1.922812612
HSAP0406S00000009 -2.321749924
HSAP0406S00000010 -2.147611982
HSAP0406S00000011 -0.663165009
HSAP0406S00000012 -2.193014297
HSAP0406S00000013 -1.904709336
HSAP0406S00000014 -0.600006793
HSAP0406S00000015 -2.077745489
HSAP0406S00000016 -2.039048858
HSAP0406S00000017 -3.524393088
HSAP0406S00000018 0.175714504
HSAP0406S00000019 -1.978472705
HSAP0406S00000020 -0.889652172
HSAP0406S00000022 -1.451674928
HSAP0406S00000025 -1.106349889
HSAP0406S00000027 -0.893655429
HSAP0406S00000029 -2.192454737
HSAP0406S00000031 -2.767513451

Total number of rows: 24134

Table truncated, full table size 720 Kbytes.




Supplementary file Size Download File type/resource
GSM601456_266016-WC-13-081217_532.pair.gz 6.2 Mb (ftp)(http) PAIR
GSM601456_266016-WC-13-081217_635.pair.gz 6.1 Mb (ftp)(http) PAIR
Processed data included within Sample table

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