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Sample GSM2592961 Query DataSets for GSM2592961
Status Public on Jul 31, 2018
Title H3K27me3 responsive AML sample 1
Sample type SRA
 
Source name bone marrow
Organism Homo sapiens
Characteristics antibody: H3K27me3
type: responsive
cell sorting: CD34+/CD38-
status: Diagnostic AML
Extracted molecule genomic DNA
Extraction protocol Samples were sheared using a Covaris sonicator until DNA reached a final size of 100-300bp. 750ng of drosophila spike in chromatin (Active Motif) was added to each sonicated sample. 4ug of anti-H3K27me3 antibody (Cell Signaling, c36B11) or H3 (Abcam, ab1791) was bound to pre-blocked Protein A7 magnetic beads (Millipore) in combination with 2ug of Spike-in antibody (Active Motif) for 12 hours. The beads were then combined with sonicated sample containing Drosophila spike in chromatin and incubated overnight. After incubation, beads were collected and DNA-antibody complexes were eluted at 65 o C. Crosslinks were reversedovernight at 65 o C. Samples were treated with Proteinase K (Fisher Scientific) and RNaseA (Fisher Scientific) and DNA was purified using phenol-chloroform. All ChIP-seq experiments were cell number normalized and 150,000 cells per biological sample were used for each H3 and H3K27me3 ChIP experiment.
For sequencing total ChIP DNA was used for library preparation (NextFlex Illumina Chip-seq kit).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Data processing Reads were mapped separately to the reference human (hg19) and Drosophila melanogaster (BDGP6.0) genome assemblies using Bowtie 2.2.6. Reads were mapped separately to the reference human (hg19) and Drosophila melanogaster (BDGP6.0) genome assemblies using Bowtie 2.2.6
Genome_build: hg19, Ensembl 67
Supplementary_files_format_and_content: peak, bigwig
 
Submission date May 01, 2017
Last update date May 15, 2019
Contact name William Stanford
E-mail(s) wstanford@ohri.ca
Phone 613-737-8899
Organization name Ottawa Hospital Research Institute
Lab Stanford
Street address 501 Smyth Road
City Ottawa
State/province Ontario
ZIP/Postal code K1H 8L6
Country Canada
 
Platform ID GPL18573
Series (2)
GSE98378 Targeting the MTF2-MDM2 Axis Sensitizes Refractory Acute Myeloid Leukemia to Chemotherapy [ChIP-Seq]
GSE98380 Targeting the MTF2-MDM2 Axis Sensitizes Refractory Acute Myeloid Leukemia to Chemotherapy
Relations
BioSample SAMN06854451
SRA SRX2771338

Supplementary file Size Download File type/resource
GSM2592961_H3K27me3-Basal-1_S12_dedup_ext200_scaled.bw 339.7 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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