NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM386205 Query DataSets for GSM386205
Status Public on Mar 25, 2009
Title EZH1 bioChIP in CJ7 cells on D chip
Sample type genomic
 
Channel 1
Source name EZH1 bioChIP in CJ7 cells (3 replicates)
Organism Mus musculus
Characteristics cell type: embryonic stem
antibody: EZH1
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 GPL6447
Series (1)
GSE15388 EZH1 and H3K27me3 ChIP-chip data from mouse embryonic stem cells

Supplementary file Size Download File type/resource
GSM386205_Input_CJ7_xs2_Mm7D.CEL.gz 22.0 Mb (ftp)(http) CEL
GSM386205_Input_bfEzh1_xs18_Mm7D.CEL.gz 23.6 Mb (ftp)(http) CEL
GSM386205_Input_ezh2m_1d_xs1_Mm7d.CEL.gz 23.9 Mb (ftp)(http) CEL
GSM386205_MAT_mm8.txt.gz 54.0 Kb (ftp)(http) TXT
GSM386205_bioEzh1_18_xs22_Mm7D.CEL.gz 27.5 Mb (ftp)(http) CEL
GSM386205_bioEzh1_20_xs23_Mm7D.CEL.gz 25.8 Mb (ftp)(http) CEL
GSM386205_bioEzh1_7_xs21_Mm7D.CEL.gz 26.5 Mb (ftp)(http) CEL
Processed data provided as supplementary file

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