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Sample GSM570360 Query DataSets for GSM570360
Status Public on Jan 01, 2012
Title Immunoprecipitated chromatin, antibody 2, replicate 2 Set 2
Sample type genomic
 
Channel 1
Source name Ramos cells, nonIP, control
Organism Homo sapiens
Characteristics cell type: Ramos germinal center B cells
cell type: Burkitt's lymphoma cell line
antibody: none
Treatment protocol Untreated cells were used for chromatin isolation.
Growth protocol Ramos cells were grown in RPMI supplemented with 10% fetal bovine serum, non-essential amino acids, and antibiotics.
Extracted molecule genomic DNA
Extraction protocol 2x10^8 cells were pelleted, washed with PBS, and lysed with hypotonic buffer on ice for 10 minutes to release the cytoplasm. Nuclei were pelleted at 4 degrees C and lysed with ice-cold nuclear lysis buffer supplemented with protease inhibitor, on ice for 10 minutes. Chromatin was sheared by sonication, using 5 pulses of 30 seconds each, separated by 1-minute rests. DNA size was analyzed on a 2% agarose gel, and appeared as a smear ranging from 0.5-1 kb.
Label Cy3
Label protocol 500ng of the control and ChIP-enriched genomic DNA was heat fragmented at 95C for 30’. The heat fragmented DNA was labeled using BioPrime DNA Labeling System (Invitrogen, Carlsbad, CA) with some modifications.
 
Channel 2
Source name Ramos cells, immunoprecipitataed, test
Organism Homo sapiens
Characteristics cell type: Ramos germinal center B cells
cell type: Burkitt's lymphoma cell line
antibody: Ab2 = EMD Biosciences #ST1099
Treatment protocol Untreated cells were used for chromatin isolation.
Growth protocol Ramos cells were grown in RPMI supplemented with 10% fetal bovine serum, non-essential amino acids, and antibiotics.
Extracted molecule genomic DNA
Extraction protocol 2x10^8 cells were pelleted, washed with PBS, and lysed with hypotonic buffer on ice for 10 minutes to release the cytoplasm. Nuclei were pelleted at 4 degrees C and lysed with ice-cold nuclear lysis buffer supplemented with protease inhibitor, on ice for 10 minutes. Chromatin was sheared by sonication, using 5 pulses of 30 seconds each, separated by 1-minute rests. DNA size was analyzed on a 2% agarose gel, and appeared as a smear ranging from 0.5-1 kb.
Label Cy5
Label protocol 500ng of the control and ChIP-enriched genomic DNA was heat fragmented at 95C for 30’. The heat fragmented DNA was labeled using BioPrime DNA Labeling System (Invitrogen, Carlsbad, CA) with some modifications.
 
 
Hybridization protocol The purified enriched and control DNA were hybridized to an Agilent 244K Human Promoter ChIP-on-chip Microarray Set (Agilent Technologies, Palo Alto, CA) using Maui AO (BioMicro Systems, Salt Lake City, UT). The microarrays were hybridized at 60º in a MAUI hybridization station on setting B (12spotMAUI) for 18 hours and then washed using Agilent aCGH wash buffers following the provided protocols.
Scan protocol Microarrays were scanned using the Agilent DNA microarray scanner, and data were extracted from images using the Agilent Feature Extraction (version 9.5.1.1) software.
Description 112707_251470711232_S01_CGH-v4_91_Amgen_082406.txt
Data processing The data were extracted using the Agilent Feature Extraction (version 9.5.1.1) software using the standard Agilent protocol with Lowess normalization.
 
Submission date Jul 26, 2010
Last update date Jan 01, 2012
Contact name Chetan Deshpande
E-mail(s) chetand@amgen.com
Organization name Amgen Inc
Department Molecular Sciences
Street address One Amgen Center Dr
City Newbury Park
State/province CA
ZIP/Postal code 91320
Country USA
 
Platform ID GPL4125
Series (2)
GSE23170 ChIP-on-chip experiment from Ramos cells to analyze genome-wide CRTC2 binding sites in germinal center B cells
GSE23171 CRTC2 couples genotoxic stress and plasma cell differentiation in the germinal center

Data table header descriptions
ID_REF
VALUE normalized log10 ratio Cy5/Cy3

Data table
ID_REF VALUE
1 -9.436306306e-001
2 0.000000000e+000
3 0.000000000e+000
4 -5.544991742e-001
5 1.451979083e-002
6 0.000000000e+000
7 -1.506878026e-001
8 -5.558155229e-002
9 -1.510590978e-001
10 -3.167546031e-001
11 3.510522053e-001
12 -3.306669254e-001
13 -1.072966815e-001
14 2.392593008e-001
15 1.635807605e-001
16 -1.517553352e-001
17 -4.120084957e-001
18 2.072036545e-001
19 -1.592532381e-001
20 2.022651332e-001

Total number of rows: 243485

Table truncated, full table size 5725 Kbytes.




Supplementary file Size Download File type/resource
GSM570360_112707_251470711232_S01_CGH-v4_91_Amgen_082406.txt.gz 68.2 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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