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Sample GSM601451 Query DataSets for GSM601451
Status Public on Feb 15, 2011
Title BCL6 ChIP-chip in BV173 cells - STI571 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: control
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
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: control
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
Hybridization protocol Standard Nimblegen protocol.
Scan protocol Standard Nimblegen protocol.
Description BV173_C_r1_WC8
BCL6 ChIP-chip in BV173 cells cultured in absence of STI571 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
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
VALUE Log2 transformed IP/INPUT(CY5/CY3)

Data table
HSAP0406S00000003 -0.301539187
HSAP0406S00000005 1.016157265
HSAP0406S00000008 0.659905779
HSAP0406S00000009 -0.228927728
HSAP0406S00000010 0.279134806
HSAP0406S00000011 -0.466569586
HSAP0406S00000012 0.014443622
HSAP0406S00000013 -0.808236206
HSAP0406S00000014 0.380015677
HSAP0406S00000015 -0.837710448
HSAP0406S00000016 0.096490213
HSAP0406S00000017 -0.848572007
HSAP0406S00000018 0.62051786
HSAP0406S00000019 0.393075117
HSAP0406S00000020 -0.283839034
HSAP0406S00000022 -0.29224257
HSAP0406S00000025 -0.589202498
HSAP0406S00000027 0.107329009
HSAP0406S00000029 -0.456163768
HSAP0406S00000031 -0.495010071

Total number of rows: 24134

Table truncated, full table size 716 Kbytes.

Supplementary file Size Download File type/resource
GSM601451_266024-WC-8-081217_532.pair.gz 6.2 Mb (ftp)(http) PAIR
GSM601451_266024-WC-8-081217_635.pair.gz 6.1 Mb (ftp)(http) PAIR
Processed data included within Sample table

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