|
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.
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|
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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 |
|