|
| Status |
Public on Dec 31, 2016 |
| Title |
BCL6 ChIP-chip in FL primary sample, FL_15 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
follicular lymphoma, input
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: primary follicular lymphoma
chip antibody: none
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Sonicated genomic DNA, then purified by Qiagen column.
|
| Label |
Cy3
|
| Label protocol |
Described in www.nimblegen.com.
|
| |
|
| Channel 2 |
| Source name |
follicular lymphoma, BCL6 ChIP
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: primary follicular lymphoma
sample identifier: WC16
chip antibody: anti-BCL6 antibody (N3)
antibody vendor: Santa Cruz Biotechnology (Santa Cruz, CA)
antibody catalog number: sc-858
antibody lot number: I2607
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin immunoprecipitation to isolate genomic regions bound by BCL6, then purify by Qiagen column.
|
| Label |
Cy5
|
| Label protocol |
Described in www.nimblegen.com.
|
| |
|
| |
| Hybridization protocol |
Described in www.nimblegen.com.
|
| Scan protocol |
Described in www.nimblegen.com.
|
| Description |
BCL6 ChIP-chip in FL primary sample - FL_15.
|
| 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 |
May 09, 2011 |
| Last update date |
Dec 31, 2016 |
| 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) |
| GSE29165 |
ChIP-on-chip of BCL6 in follicular lymphoma |
|
