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Sample GSM2054691 Query DataSets for GSM2054691
Status Public on Mar 12, 2016
Title 46c_H3K64ac_rep1
Sample type SRA
Source name 46c_H3K64ac
Organism Mus musculus
Characteristics cell line: 46c (sox1-GFP)
cell type: mouse embryonic stem cells
passages: 25-28
chip antibody: anti-H3K64ac (Di Cerbo et al 2014, PMID: 24668167)
Treatment protocol Undifferentiated ESCs and K562 cells
Growth protocol 46c (Sox1-GFP) ESCs (Ying et al. Nature biotechnology 2003) were cultivated without feeders in GMEM media containing With L-Glutamine media containing 10% fetal bovine serum (FBS), L-glutamine, Sodium Pyruvate, Lif, beta-Mercaptoethanol, Nonessential aminoacids, penicillin and streptomycin. Human erythro-myeloblastoid leukemia cells (K562) were cultured in RPMI 1640 With L-Glutamine media containing 10% fetal bovine serum (FBS), L-glutamine, penicillin and streptomycin.
Extracted molecule genomic DNA
Extraction protocol Chromatin was digested with MNase and released at 4C overnight, then histone-DNA complexes were isolated with antibody
DNA libraries were prepared for sequencing using standard Illumina protocols
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
Description processed data file:
46C_H3K64acmerged.10bpres.bed, 46C_H3K64acmerged.10bpres.bedGraph.gz
Data processing ChIP-seq reads were aligned to the mm9 genome assembly using bowtie-0.12.8 (options bowtie -e 40 -m 1 -v 2)
Bedgraph tracks were generated from the aligned reads by the program makeUCSC file from HOMER software suite (version 4.3) at a resolution of 10bp and the total number of tags is normalized to 10 million.
bed peak files were generated using SICER (v1.1) (Zang et al, 2009), using GSM1156619 UD46c input as control library, a window size of 200bp, gap size of 600bp and and FDR of 0.01
column headers for islands-summary-FDR0.01.bed files;
Genome_build: 46c data: NCBI37/mm9; K562 data: GRCh37/hg19
Submission date Feb 04, 2016
Last update date May 15, 2019
Contact name Pradeepa M Madapura
Organization name Queen Mary University of London
Lab Pradeepa Madapura
Street address 4 Newark Street, Whitechapel
City London
State/province UK
ZIP/Postal code E1 2AT
Country United Kingdom
Platform ID GPL13112
Series (1)
GSE66023 Histone H3 globular domain acetylation identifies new class of enhancers
BioSample SAMN04456552
SRA SRX1560889

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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