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Sample GSM721826 Query DataSets for GSM721826
Status Public on Dec 31, 2016
Title BCL6 ChIP-chip in FL primary sample, FL_19
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: WC19
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_19.
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 -2.262118253
HSAP0406S00000005 0.709765735
HSAP0406S00000008 -0.602911084
HSAP0406S00000009 -1.755348012
HSAP0406S00000010 -1.570596808
HSAP0406S00000011 -2.084333704
HSAP0406S00000012 -1.505889198
HSAP0406S00000013 -2.373548937
HSAP0406S00000014 -2.024701318
HSAP0406S00000015 -2.672300934
HSAP0406S00000016 -1.377722731
HSAP0406S00000017 -2.502598095
HSAP0406S00000018 0.060212594
HSAP0406S00000019 0.090756797
HSAP0406S00000020 -0.556599447
HSAP0406S00000022 -1.599553328
HSAP0406S00000025 -0.364648504
HSAP0406S00000027 -0.1808945
HSAP0406S00000029 -2.460781065
HSAP0406S00000031 0.213514685

Total number of rows: 24134

Table truncated, full table size 720 Kbytes.




Supplementary file Size Download File type/resource
GSM721826_268780S-WC-19-090112_532.pair.gz 6.2 Mb (ftp)(http) PAIR
GSM721826_268780S-WC-19-090112_635.pair.gz 6.2 Mb (ftp)(http) PAIR
Processed data included within Sample table

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