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Sample GSM243192 Query DataSets for GSM243192
Status Public on Jan 30, 2008
Title hScc1 localization in G2 (Whole Genome #3)
Sample type genomic
 
Channel 1
Source name Chromatin Immuno-precipitated DNA
Organism Homo sapiens
Characteristics HeLa cells. Anti-hScc1 atibody was used for Chromatin immuno-precipitation
Extracted molecule genomic DNA
Extraction protocol Cells at 70-80% confluency were crosslinked with 1% formaldehyde for 10 min and after quenching with 125 mM glycine prepared for ChIP. Chromatin immunoprecipitation was performed using Scc1, Smc3, CTCF, SA2 and control antibodies. The lysate was incubated with the antibodies over night. Then the pre-absorbed protein A Affiprep beads (Bio-Rad) were added and incubated for 2 hours at 4 degree. The beads were washed several times and eluted for 20 min at 65 degree with elution buffer (50 mM Tris, 10 mM EDTA, 1 % SDS). The eluate from the beads was treated with Proteinase K and decrosslinked at 65°C over night. Contaminating RNA was removed by RNAse treatment. Then the sample was further purified by phenol-chloroform extraction and one additional purification step using the PCR purification kit (Qiagen).
Label Biotin-11-ddATP
Label protocol DNA was amplified by IVT (In vitro transcription) method. For the labeling, DNA was fragmented by DNaseI. DNA was end-labeled by Terminal Transferase with biotin‐N11‐ddATP (NEL508).
 
Channel 2
Source name Whole cell extract (WCE) fraction used for the normalization of ChIP fraction.
Organism Homo sapiens
Characteristics HeLa cells
Extracted molecule genomic DNA
Extraction protocol same as channel 1
Label Biotin-11-ddATP
Label protocol same as channel 1
 
 
Hybridization protocol Each sample was hybridized to the array in 200 ul containing 1XHybridization buffer (Affymetrix), 50pM Control oligonucleotide (oligo B2, Affymetrix), Herring Sperm DNA (0.1mg/ml), Acetylated BSA (0.5mg/ml), and 7% DMSO. Samples were denatured at 100C for 10 minutes, and then put on ice before being hybridized for 16 hours at 45C in an hybridization oven (GeneChip Hybridization Oven 640, Affymetrix). Washing and scanning protocol provided by Affymetrix was performed automatically on a fluidics station (GeneChip fluidics station 450, Affymetrix).
Scan protocol Arrays were scanned using the Genechip Scanner3000 7G following the library array description.
Description hScc1 distribution in G2 phase. Array 3 of 14.
Data processing Array intensity data from duplicated experiments of ChIP and WCE fraction were compared by MAT (Model-based Analysis of Tiling-array) algorithm, using the software provided by the laboratory of X.Shirley Liu (http://chip.dfci.harvard.edu/~wli/MAT/). We calculated MAT score and mapped the results to genomic positions in human genome assembly hg 17 (NCBI Build 36). Bandwidth, MaxGap, and MinProbe parameters were set to 250, 1000, and 12, respectively. Cutoff threshold p-values were set to 1.0e-10, 1.0e-8, and 5.0e-8 for ENCODE1.0, 2.0, and Human Tiling 1.0R, respectively.
For ChIP-chip analysis, we use two IP .CEL files and two WCE .CEL files (they are duplicated experiments) to make one profile.
 
Submission date Nov 15, 2007
Last update date Aug 14, 2011
Contact name Katsuhiko Shirahige
E-mail(s) kshirahi@iam.u-tokyo.ac.jp
Phone +81-3-5842-0756
Fax +81-3-5842-0757
URL http://www.iam.u-tokyo.ac.jp/chromosomeinformatics/
Organization name The University of Tokyo
Department Research Center for Epigenetic Disease
Lab Laboratory of Genome Structure and Function
Street address 1-1-1 Yayoi
City Bunkyo-ku
State/province Tokyo
ZIP/Postal code 113-0032
Country Japan
 
Platform ID GPL6133
Series (1)
GSE9613 Cohesin mediates transcriptional insulation by CCCTC-binding factor

Data table header descriptions
ID_REF
VALUE MAT Score

Data table
ID_REF VALUE
2_2812 0.00000
2_2521835 0.00000
2_3714382 0.00000
2_4155031 0.00000
2_4155238 0.00000
2_4155558 0.00000
2_4155741 0.00000
2_4419191 0.00000
2_4539363 0.00000
2_4539448 0.00000
2_4698697 0.00000
2_5370806 0.00000
2_6152770 0.00000
2_6972851 0.00000
2_7382516 0.00000
2_8256751 0.00000
2_8256786 0.00000
2_8256823 0.00000
2_8256899 0.00000
2_8739745 0.00000

Total number of rows: 3095816

Table truncated, full table size 59965 Kbytes.




Supplementary file Size Download File type/resource
GSM243192.CEL.gz 26.2 Mb (ftp)(http) CEL
GSM243192_1.CEL.gz 25.6 Mb (ftp)(http) CEL
GSM243192_2.CEL.gz 25.9 Mb (ftp)(http) CEL
GSM243192_3.CEL.gz 25.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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