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Sample GSM4368652 Query DataSets for GSM4368652
Status Public on Dec 21, 2022
Title BMDM_PRX_LPS0h_rep3
Sample type SRA
 
Source name Bone marrow-derived macrophage
Organism Mus musculus
Characteristics strain: C57BL/6
Treatment protocol For LPS treatment, 100 ng/ml of LPS (Sigma-Aldrich) was added to the medium.
Growth protocol Bone marrow cells were flushed from femurs and tibias of male mice between 6 and 9 weeks of age, and were grown in RPMI (Nacalai Tesque) supplemented with 10% FBS (HyClone), 1% penicillin–streptomycin (Thermo Fisher), 1% L-glutamine (Thermo Fisher), and 40 ng/ml of recombinant mouse M-CSF (576406; BioLegend) for 7-8 days. The medium was changed every 3 days. Differentiated BMDMs were detached from plates using PBS supplemented with 2% EDTA and replated into 12-well tissue culture dishes at a density of 5 x 105 cells per well prior to cell stimulation.
Extracted molecule total RNA
Extraction protocol Poly-A mRNA was extracted from total RNA by using an NEBNext Poly(A) mRNA magnetic Isolation module (NEB), after which RNA-seq libraries were prepared using a NEBNext UltraII RNA Library Prep kit for Illumina (NEB) according to the manufacturer’s protocol.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Description PRX-treated, LPS-untreated
Data processing Reads were aligned to the mm9 mouse genome using STAR.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files were generated using Homer.
 
Submission date Mar 02, 2020
Last update date Dec 21, 2022
Contact name Ichiro Manabe
E-mail(s) manabe-tky@umin.ac.jp
Organization name Chiba University
Street address 1-8-1 Inohana, Chuo
City Chiba
ZIP/Postal code 260-8670
Country Japan
 
Platform ID GPL18480
Series (1)
GSE146236 Analysis of effects of polyrotaxane on macrophages
Relations
BioSample SAMN14259016
SRA SRX7827878

Supplementary file Size Download File type/resource
GSM4368652_BMDM_PRX_LPS0h_rep3.bedGraph.gz 59.4 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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