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Sample GSM2522445 Query DataSets for GSM2522445
Status Public on Aug 31, 2017
Title PolyA RNA-seq BmalKO KLA0h
Sample type SRA
 
Source name mouse BMDM
Organism Mus musculus
Characteristics strain: C57BL/6J
tissue: bone marrow-derived macrophage
treatment: KLA 0h
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 polyA RNA
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 RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
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 GPL13112
Series (1)
GSE95712 Bmal1 regulates inflammatory response in macrophage
Relations
BioSample SAMN06480876
SRA SRX2613932

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

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