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Sample GSM601449 Query DataSets for GSM601449
Status Public on Feb 15, 2011
Title BCL6 ChIP-chip in NALM1 cells - STI571 replicate 1
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
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
Hybridization protocol Standard Nimblegen protocol.
Scan protocol Standard Nimblegen protocol.
Description NALM1_C_r1_WC6
BCL6 ChIP-chip in NALM1 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 -0.580973716
HSAP0406S00000005 1.416589672
HSAP0406S00000008 -0.311723402
HSAP0406S00000009 -0.897971256
HSAP0406S00000010 0.439832635
HSAP0406S00000011 -0.506067601
HSAP0406S00000012 -0.039244785
HSAP0406S00000013 -0.5266802
HSAP0406S00000014 -0.324986117
HSAP0406S00000015 -0.582399099
HSAP0406S00000016 0.156697129
HSAP0406S00000017 -1.511141838
HSAP0406S00000018 0.224098931
HSAP0406S00000019 -0.901124475
HSAP0406S00000020 0.013401228
HSAP0406S00000022 -0.291448679
HSAP0406S00000025 0.225503681
HSAP0406S00000027 0.131270384
HSAP0406S00000029 -0.226481065
HSAP0406S00000031 0.033729843

Total number of rows: 24134

Table truncated, full table size 717 Kbytes.

Supplementary file Size Download File type/resource
GSM601449_268776-WC-6-081222_532.pair.gz 6.2 Mb (ftp)(http) PAIR
GSM601449_268776-WC-6-081222_635.pair.gz 6.1 Mb (ftp)(http) PAIR
Processed data included within Sample table

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