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Sample GSM601447 Query DataSets for GSM601447
Status Public on Feb 15, 2011
Title BCL6 ChIP-chip in Tom1 cells - STI571 replicate 1
Sample type genomic
Channel 1
Source name genomic DNA [input]
Organism Homo sapiens
Characteristics cell type: Ph+ ALL cell line TOM-1
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 TOM-1
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 TOM1_C_r1_WC4
BCL6 ChIP-chip in Tom1 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 0.62247729
HSAP0406S00000005 1.976025847
HSAP0406S00000008 0.864845108
HSAP0406S00000009 -1.303997721
HSAP0406S00000010 0.160271437
HSAP0406S00000011 -0.130875138
HSAP0406S00000012 0.004366675
HSAP0406S00000013 -0.305135271
HSAP0406S00000014 0.642051909
HSAP0406S00000015 -0.024735391
HSAP0406S00000016 0.186973685
HSAP0406S00000017 -0.365665917
HSAP0406S00000018 0.847143562
HSAP0406S00000019 -0.084519457
HSAP0406S00000020 -0.381222434
HSAP0406S00000022 1.238445752
HSAP0406S00000025 0.009222108
HSAP0406S00000027 -0.723689045
HSAP0406S00000029 -0.519630018
HSAP0406S00000031 0.089052393

Total number of rows: 24134

Table truncated, full table size 715 Kbytes.

Supplementary file Size Download File type/resource
GSM601447_268785-WC-4-081210_532.pair.gz 6.2 Mb (ftp)(http) PAIR
GSM601447_268785-WC-4-081210_635.pair.gz 6.1 Mb (ftp)(http) PAIR
Processed data included within Sample table

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