|
| Status |
Public on Nov 27, 2012 |
| Title |
MYC ChIP-chip in ramos cells, replicate 1 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
ramos cells, input
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: ramos
cell type: Burkitt lymphoma cells
genotype: Ph+
chip antibody: none
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Sonicated genomic DNA, and then purified by Qiagen column. The detailed method was published in Polo et al. Proc Natl Acad Sci U S A. 2007 Feb 27;104(9):3207-12 (PMID 17360630).
|
| Label |
Cy3
|
| Label protocol |
Described in www.nimblegen.com
|
| |
|
| Channel 2 |
| Source name |
ramos cells, MYC ChIP
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: ramos
cell type: Burkitt lymphoma cells
chip antibody: rabbit anti-c-MYC (N-262) polyclonal
antibody vendor: Santa Cruz Biotechnology
antibody catalog number: sc-764
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin immunoprecipitation to isolate genomic regions bound by MYC, and then purified by Qiagen column. The detailed method was published in Polo et al. Proc Natl Acad Sci U S A. 2007 Feb 27;104(9):3207-12 (PMID 17360630).
|
| Label |
Cy5
|
| Label protocol |
Described in www.nimblegen.com
|
| |
|
| |
| Hybridization protocol |
Described in www.nimblegen.com
|
| Scan protocol |
Described in www.nimblegen.com
|
| Description |
MYC ChIP-chip in ramos cells - replicate 1 of 2.
|
| Data processing |
Take all the probes in the promoter region and perform log2 transformation of IP/INPUT (Cy5/Cy3). Then use the maximal summary of three connected probes as the bound intensity of the promoter. The detailed analysis method (script) was published in Ci et al. Blood. 2009 May 28;113(22):5536-48 (PMID 19307668).
|
| |
|
| Submission date |
Aug 01, 2011 |
| Last update date |
Nov 27, 2012 |
| 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 (1) |
| GSE31110 |
Recruitment of MYC to target genes in ramos and mutu3 cells |
|
