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Sample GSM310414 Query DataSets for GSM310414
Status Public on Nov 04, 2008
Title MLL-rearranged_ALL_H3K79 (5 samples)
Sample type genomic
Source name H3K79me2 ChIP of MLL-rearranged ALL bone marrow
Organism Homo sapiens
Characteristics MLL-rearranged ALL bone marrow
Extracted molecule genomic DNA
Extraction protocol 3-10×10e5 cells were used. Briefly, cells were cross-linked by addition of 1% formaldehyde for 10 min at room temp. Cross-linking was terminated by adding final 125 mM glycine and cells were washed with cold PBS containing PMSF, collected by centrifugation and washed in PBS twice. The pellet was resuspended in SDS buffer (50 mM Tris-Cl pH 8.1; 100 mM NaCl; 0.5% SDS; 5 mM EDTA; 0.2% NaN3 and protease inhibitors) and snap frozen. After thawing the nuclear pellets were collected by centrifugation and resuspended in ChIP buffer (50mM Tris 8.1; 100mM NaCl; 0.3% SDS; 1.5% Triton X-100; 5 mM EDTA; 0.2% NaN3; and protease inhibitors). Cells were sonicated to fragment DNA to an average size of 0.5-1 kb. The sample was centrifuged at 10000g at 4° C for 10 min, the supernatant collected and pre-cleared with protein-A beads at 4°C for 2 hrs. The sample was then incubated with anti-dimethyl H3K79 antibody (ab# ab3594) and protein-A beads at 4°C overnight. Immunoprecipitated protein-DNA complexes were sequentially washed with Mixed Micelle buffer (20 mM Tris pH 8.1; 150mM NaCl; 5mM EDTA; 0.5% SDS; 1% Triton X-100; 6% Sucrose), buffer 500 (0.1% Deoxycholate, 1% Triton X-100, 1 mM EDTA, 50 mM HEPES pH 7.5, 500 mM NaCl), LiCl buffer (250 mM LiCl, 0.5% NP-40, 0.5% Deoxycholate, 1 mM EDTA, 10 mM Tris-Cl pH 8.1) and TE buffer (10 mM Tris-Cl pH 7.5, 1 mM EDTA). All washes were for 5 min at 4C. Protein-DNA complexes were eluted in TE with 1%SDS buffer supplemented with proteinase K (500u) for 3 hrs at 55oC. The sample was treated with RNase A and DNA fragments were purified using Qiagen's PCR purification kit, and eluted in 100 ul of TE buffer.
Label Biotin
Label protocol Each ChIP was amplified using ligation-mediated PCR (LM-PCR). Labeling was according to standard Affymetrix protocols.
Hybridization protocol 3 micrograms of labelled material was hybridized according to the standard Affymetrix protocol.
Scan protocol Standard Affymetrix protocol
Description MLL-rearranged ALL H3K79 CHIP: MLL-AF4_061505_HsProm.CEL, MLL-AF4_A37_HsProm.CEL, MLL-AF4_06078_HsProm.CEL, MLL-ENL_06078_HsProm.CEL, MLL-AF4_05015_HsProm.CEL
Data processing Regions of above-background signal were identified by Model-based Analysis of Tiling array (MAT) software ( run with bandwidth = 300, max gap = 300, minimum probes = 10 and p-value cutoff = 1x10e-5 and using a bpmap for human NCBI genome build 36 (Hg18) downloaded from the MAT website.
Submission date Aug 06, 2008
Last update date Nov 04, 2008
Contact name Madeleine E. Lemieux
Phone 617-595-6695
Organization name Bioinfo
Street address 275 Main St., Suite 252
City Plantagenet
State/province ON
ZIP/Postal code K0B 1L0
Country Canada
Platform ID GPL5082
Series (2)
GSE12360 Genome-wide analysis of H3K79 methylation in CD34+ CD19+ cells from normal marrow, MLL-rearranged or MLL-germline ALL
GSE12363 H3K79 methylation profiles define murine and human MLL-AF4 leukemias

Supplementary file Size Download File type/resource
GSM310414_MLL-AF4_05015_HsProm.CEL.gz 17.6 Mb (ftp)(http) CEL
GSM310414_MLL-AF4_06078_HsProm.CEL.gz 19.7 Mb (ftp)(http) CEL
GSM310414_MLL-AF4_061505_HsProm.CEL.gz 18.0 Mb (ftp)(http) CEL
GSM310414_MLL-AF4_A37_HsProm.CEL.gz 17.9 Mb (ftp)(http) CEL
GSM310414_MLL-ENL_06078_HsProm.CEL.gz 18.6 Mb (ftp)(http) CEL 23.5 Mb (ftp)(http) BAR
GSM310414_MLL-r_ALL.bed.gz 142.1 Kb (ftp)(http) BED
Processed data provided as supplementary file

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