NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM721824 Query DataSets for GSM721824
Status Public on Dec 31, 2016
Title BCL6 ChIP-chip in FL primary sample, FL_16
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: WC17
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_16.
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

Data table header descriptions
ID_REF
VALUE Log2-transformed ratio (IP/Input)

Data table
ID_REF VALUE
HSAP0406S00000003 -4.44058403
HSAP0406S00000005 0.718838579
HSAP0406S00000008 -4.082200391
HSAP0406S00000009 -3.53787296
HSAP0406S00000010 -3.883839589
HSAP0406S00000011 -3.383491889
HSAP0406S00000012 -4.89238852
HSAP0406S00000013 -4.688405774
HSAP0406S00000014 -3.338780361
HSAP0406S00000015 -4.849733262
HSAP0406S00000016 -3.90778958
HSAP0406S00000017 -3.250716012
HSAP0406S00000018 -0.091782796
HSAP0406S00000019 -6.246479152
HSAP0406S00000020 -3.112173538
HSAP0406S00000022 -3.671885126
HSAP0406S00000025 -1.656707467
HSAP0406S00000027 -3.17695487
HSAP0406S00000029 -4.334575479
HSAP0406S00000031 -4.526770103

Total number of rows: 24134

Table truncated, full table size 722 Kbytes.




Supplementary file Size Download File type/resource
GSM721824_268781S-WC-17-090112_532.pair.gz 6.3 Mb (ftp)(http) PAIR
GSM721824_268781S-WC-17-090112_635.pair.gz 6.2 Mb (ftp)(http) PAIR
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap