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Sample GSM3728651 Query DataSets for GSM3728651
Status Public on Jul 08, 2020
Title BMDM_LPS4h
Sample type SRA
 
Source name Bone marrow-derived macrophage
Organism Mus musculus
Characteristics strain: C57BL/6
genotype/variation: wild-type
treatment: LPS 4h
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 DMEM/F12 (Thermo Fisher) 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 StemPro Accutase Cell Dissociation Reagent (Thermo Fisher) 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 Oligo-dT beads of TruSeq RNA Sample Prep Kit v2 (Illumina), after which RNA-seq libraries were prepared using a ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre) according to the manufacturer’s protocol.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer IIx
 
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 Apr 17, 2019
Last update date Jul 08, 2020
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 GPL11002
Series (2)
GSE129961 Analysis of lncRNAs in macrophages
GSE130056 Analysis of long noncoding RNAs in macrophages
Relations
BioSample SAMN11456316
SRA SRX5704445

Supplementary file Size Download File type/resource
GSM3728651_BMDM_LPS4h.ucsc.bedGraph.gz 57.7 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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