NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2522474 Query DataSets for GSM2522474
Status Public on Aug 31, 2017
Title ChIP-seq p65 WT KLA12h
Sample type SRA
 
Source name mouse BMDM
Organism Mus musculus
Characteristics strain: C57BL/6J
tissue: bone marrow-derived macrophage
treatment: KLA 12h
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 (http://homer.salk.edu/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 (http://homer.salk.edu/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
E-mail(s) yuooishi-circ@umin.ac.jp
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
Relations
BioSample SAMN06480851
SRA SRX2613961

Supplementary file Size Download File type/resource
GSM2522474_p65ChIP_BMDM_WT_KLA12h.ucsc.bedGraph.gz 48.0 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap