|
| 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 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_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 |
| 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 |
|
