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Sample GSM386194 Query DataSets for GSM386194
Status Public on Mar 25, 2009
Title H3K27me3 ChIP in CJ7 cells on G chip
Sample type genomic
 
Channel 1
Source name H3K27me3 ChIP in CJ7 cells (3 replicates)
Organism Mus musculus
Characteristics cell type: embryonic stem
antibody: H3K27me3
cell line: CJ7
genotype: wild-type
Treatment protocol wild-type (WT) and Ezh2-/- mutant ES cells were fixed with 0.8% formaldehyde for 10 min at room temperature. Cell lydates were ChIP'ed by antibody recognizing H3K27me3 mark (Upstate) or by using streptavidin-Dyna beads (Invitrogen). DNA fragments were isolated and amplified by LM-PCR. Amplified DNA was fragmented and biotin labeled before hybridiztion.
Growth protocol standard culture conditions were used to culture ES cells.
Extracted molecule genomic DNA
Extraction protocol pulled down chromatin was reversely crosslinked and DNA was precipitated by isopropanol.
Label biotin
Label protocol Fragmented DNA was labeled with biotin-N6-ddATP by terminal deoxynucleiotidyl transferase.
 
Channel 2
Source name INPUT CONTROL
Organism Mus musculus
Characteristics input 1: genomic DNA from J1 cells expressing bfEZH1
input 2: genomic DNA from CJ7 cells
input 3: genomic DNA from Ezh2-/- cells
Treatment protocol wild-type (WT) and Ezh2-/- mutant ES cells were fixed with 0.8% formaldehyde for 10 min at room temperature. Cell lydates were ChIP'ed by antibody recognizing H3K27me3 mark (Upstate) or by using streptavidin-Dyna beads (Invitrogen). DNA fragments were isolated and amplified by LM-PCR. Amplified DNA was fragmented and biotin labeled before hybridiztion.
Growth protocol standard culture conditions were used to culture ES cells.
Extracted molecule genomic DNA
Extraction protocol pulled down chromatin was reversely crosslinked and DNA was precipitated by isopropanol.
Label biotin
Label protocol Fragmented DNA was labeled with biotin-N6-ddATP by terminal deoxynucleiotidyl transferase.
 
 
Hybridization protocol About 2-4 ug of labeled DNA were hybridized for 16 hr at 45C on tiling arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
Description ChIP-chip
Data processing The data were analyzed with Model-based Analysis of Tiling-arrays for ChIP-chip (MAT) developed by the Liu lab and processed based on MM8 annotation. MATScore, p value (in form of -10log10_Pvalue), fold-change, FDR, peak position and length were reported for each peak identified by MAT program (results provided as supplementary text files).
 
Submission date Mar 25, 2009
Last update date Mar 25, 2009
Contact name Xiaohua Shen
E-mail(s) shen@bloodgroup.tch.harvard.edu
Phone 617-632-6496
Organization name Dana Farber Cancer Institute
Department Pediatric Oncology
Lab Stuart Orkin lab
Street address 44 Binney Street
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platform ID GPL6450
Series (1)
GSE15388 EZH1 and H3K27me3 ChIP-chip data from mouse embryonic stem cells

Supplementary file Size Download File type/resource
GSM386194_3mk27a_CJ7_4g_xs24_Mm7g.CEL.gz 24.1 Mb (ftp)(http) CEL
GSM386194_3mk27b_CJ7_6g_xs26_Mm7g.CEL.gz 22.4 Mb (ftp)(http) CEL
GSM386194_3mk27k_CJ7_5g_xs25_Mm7g_MBR.CEL.gz 25.0 Mb (ftp)(http) CEL
GSM386194_Input_CJ7_xs2_Mm7G.CEL.gz 21.3 Mb (ftp)(http) CEL
GSM386194_Input_bfEzh1_xs18_Mm7G.CEL.gz 24.8 Mb (ftp)(http) CEL
GSM386194_Input_ezh2m_1g_xs1_Mm7g.CEL.gz 23.4 Mb (ftp)(http) CEL
GSM386194_MAT_mm8.txt.gz 40.5 Kb (ftp)(http) TXT
Processed data provided as supplementary file

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