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Sample GSM601455 Query DataSets for GSM601455
Status Public on Feb 15, 2011
Title BCL6 ChIP-chip in NALM1 cells - STI571 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: 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 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: 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 www.nimblegen.com
 
 
Hybridization protocol Standard Nimblegen protocol.
Scan protocol Standard Nimblegen protocol.
Description NALM1_C_r2_WC12
BCL6 ChIP-chip in NALM1 cells cultured in absence of STI571 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 -2.266140681
HSAP0406S00000005 0.812053261
HSAP0406S00000008 -1.57182945
HSAP0406S00000009 -0.146712173
HSAP0406S00000010 -1.001195471
HSAP0406S00000011 -1.814203652
HSAP0406S00000012 -2.041689133
HSAP0406S00000013 -1.564364996
HSAP0406S00000014 -1.790060369
HSAP0406S00000015 -1.80960643
HSAP0406S00000016 -1.124155717
HSAP0406S00000017 -3.928304576
HSAP0406S00000018 -0.30887348
HSAP0406S00000019 -1.071989574
HSAP0406S00000020 -2.635232529
HSAP0406S00000022 -2.361446946
HSAP0406S00000025 -1.332159346
HSAP0406S00000027 -0.954646881
HSAP0406S00000029 -1.453440657
HSAP0406S00000031 -2.798558372

Total number of rows: 24134

Table truncated, full table size 721 Kbytes.




Supplementary file Size Download File type/resource
GSM601455_266020-WC-12-081217_532.pair.gz 6.2 Mb (ftp)(http) PAIR
GSM601455_266020-WC-12-081217_635.pair.gz 6.1 Mb (ftp)(http) PAIR
Processed data included within Sample table

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