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Sample GSM601458 Query DataSets for GSM601458
Status Public on Feb 15, 2011
Title BCL6 ChIP-chip in BV173 cells + 10µM STI571 (24h) replicate 2
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_r2_WC15
BCL6 ChIP-chip in BV173 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 -2.182928348
HSAP0406S00000005 2.032514134
HSAP0406S00000008 -1.48355796
HSAP0406S00000009 -2.594013557
HSAP0406S00000010 -1.861715967
HSAP0406S00000011 -0.308453608
HSAP0406S00000012 -1.908743752
HSAP0406S00000013 -2.413573288
HSAP0406S00000014 -0.188226379
HSAP0406S00000015 -2.061639685
HSAP0406S00000016 -1.856764516
HSAP0406S00000017 -1.886835969
HSAP0406S00000018 0.679226112
HSAP0406S00000019 -2.258132071
HSAP0406S00000020 -0.763574213
HSAP0406S00000022 -1.454740732
HSAP0406S00000025 -1.118380023
HSAP0406S00000027 -0.901568616
HSAP0406S00000029 -1.706334687
HSAP0406S00000031 -2.465221151

Total number of rows: 24134

Table truncated, full table size 720 Kbytes.




Supplementary file Size Download File type/resource
GSM601458_266261-WC-15-081217_532.pair.gz 6.2 Mb (ftp)(http) PAIR
GSM601458_266261-WC-15-081217_635.pair.gz 6.2 Mb (ftp)(http) PAIR
Processed data included within Sample table

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