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Sample GSM2522463 Query DataSets for GSM2522463
Status Public on Aug 31, 2017
Title ChIP-seq H3K27Ac WT KLA24h
Sample type SRA
Source name mouse BMDM
Organism Mus musculus
Characteristics strain: C57BL/6J
tissue: bone marrow-derived macrophage
treatment: KLA 24h
Treatment protocol Mouse macrophages are treated with bacterial lipopolysaccharide (LPS) or Kdo2-Lipid A,chemically defined substructure of LPS specifically recognized by Toll-like receptor 4 for indicated time.
Growth protocol Mouse thioglycollate-elicited macrophages and bone marrow-derived macrophages were isolated from male 6- to 9-weeks old C57BL/6J (Charles River laboratories) and Arntl-/- mice. Cells are cultured in RPMI-1640 medium containing 10% FCS. M-CSF (20ug/ml) was added for BMDM culture medium for 6 days.
Extracted molecule genomic DNA
Extraction protocol ChIP-Seq: Sequencing libraries were prepared from collected DNA by using NEB next Ultra DNA library prep kit for Illumina. Libraries were PCR-amplified for 12-15 cycles and sequenced on a Hi-Seq 1500 (Illumina) for 51 cycles.
RNA-Seq: PolyA-tagged RNA was pulled down with oligo-dT magnetic beads from total RNA. RNA-seq libraries were multiplexed and prepared according to the manufacturer's protocol (NEB cat#E7530, Ipswich, MA). Libraries were paired-ended sequenced on a HiSeq 2000 sequencer (Illumina, San Diego, CA)
Reads were aligned to mm9 genome using default parameter for RNA-star. Aligned reads read files were analyzed with HOMER ( to calculate RPKM from the gene bodies of RefSeq genes, perform motif analysis in the study. Reads counts were normalized using DESeq2.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 1500
Description formaldehyde cross-linked
Data processing For ChIP-Seq and RNA-Seq samples, reads were aligned to the mm9 genome using RNA-Star. Aligned read files were analyzed with HOMER ( to find peaks, calculate RPKM from the gene bodies of RefSeq genes, perform motif- and other analyses in the study.
Genome_build: mm9
Submission date Mar 06, 2017
Last update date May 15, 2019
Contact name Yumiko Oishi
Organization name Tokyo Medical and Dental University
Department Department of Cellular and Molecular Medicine
Street address 1-5-45, Yushima
City Bunkyo
State/province Tokyo
ZIP/Postal code 113-8510
Country Japan
Platform ID GPL18480
Series (1)
GSE95712 Bmal1 regulates inflammatory response in macrophage
BioSample SAMN06480867
SRA SRX2613950

Supplementary file Size Download File type/resource
GSM2522463_H3K27Ac_BMDM_WT_24.ucsc.bedGraph.gz 169.9 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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