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Sample GSM3660037 Query DataSets for GSM3660037
Status Public on Sep 05, 2019
Title H3K27ac_WT_LGMP_2
Sample type SRA
 
Source name WT LGMP cells
Organism Mus musculus
Characteristics strain: C57BL/6
chip-antibody: H3K27ac (D5E4, #8173, CST, Danvers, MA)
genotype: wild type
cell type: leukemia-GMP
Treatment protocol L-GMP cells were isolated from AMPK WT and KO mice.
Extracted molecule genomic DNA
Extraction protocol 50,000 WT or KO L-GMP cells were sorted and treated with Mnase, histone-DNA complexes were isolated with antibody
ChIP DNA was purified for end repair, adapter ligation, and amplification using a NEB Ultra II library preparation kit following the manufacturer’s protocols (New England BioLabs, Ipswich, MA)
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NovaSeq 6000
 
Data processing Basecalling and fastq generation were performed using Illumina’s software (Casava, bcl2fastq)
Reads were trimmed for quality using Trimmomatic (version 0.36)
Trimmed reads were aligned to mm10 using bowtie2 (version 2.2.6)
bedGraph files were generated using deepTools (version 3.1.0; bamCoverage)
Peak calling, enhancer, and super-enhancer predictions were performed using HOMER (version 4.10)
Genome_build: mm10
Supplementary_files_format_and_content: UCSC formatted bedGraph files, generated using deepTools (bamCoverage); scores are CPM normalized.
 
Submission date Mar 07, 2019
Last update date Sep 07, 2019
Contact name Daisuke Nakada
E-mail(s) nakada@bcm.edu
Organization name Baylor College of Medicine
Department Molecular and Human Genetics
Street address One Baylor Plaza
City Houston
State/province Texas
ZIP/Postal code 77030
Country USA
 
Platform ID GPL24247
Series (2)
GSE128000 AMPK links acetyl-coA homeostasis to BET recruitment in acute myeloid leukemia: ChIP-seq
GSE128001 AMPK links acetyl-coA homeostasis to BET recruitment in acute myeloid leukemia
Relations
BioSample SAMN11082580
SRA SRX5492031

Supplementary file Size Download File type/resource
GSM3660037_H3K27ac_WT_2.CPM.UCSC.bedgraph.gz 58.0 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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