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Sample GSM601454 Query DataSets for GSM601454
Status Public on Feb 15, 2011
Title BCL6 ChIP-chip in Tom1 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 TOM-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 TOM-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 TOM1_S_r2_WC11
BCL6 ChIP-chip in Tom1 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 -2.02227769
HSAP0406S00000005 2.269035342
HSAP0406S00000008 -1.937358771
HSAP0406S00000009 -1.954427211
HSAP0406S00000010 -1.660905214
HSAP0406S00000011 -0.822268062
HSAP0406S00000012 -1.538359244
HSAP0406S00000013 -2.404433731
HSAP0406S00000014 -1.059812502
HSAP0406S00000015 -2.594663468
HSAP0406S00000016 -1.747505341
HSAP0406S00000017 -2.129200025
HSAP0406S00000018 1.307388862
HSAP0406S00000019 -0.035725206
HSAP0406S00000020 -0.933589375
HSAP0406S00000022 -1.980780566
HSAP0406S00000025 -1.243133989
HSAP0406S00000027 -0.416695952
HSAP0406S00000029 -2.005642339
HSAP0406S00000031 -2.140891922

Total number of rows: 24134

Table truncated, full table size 719 Kbytes.




Supplementary file Size Download File type/resource
GSM601454_266022-WC-11-081217_532.pair.gz 6.2 Mb (ftp)(http) PAIR
GSM601454_266022-WC-11-081217_635.pair.gz 6.1 Mb (ftp)(http) PAIR
Processed data included within Sample table

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