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Sample GSM4453906 Query DataSets for GSM4453906
Status Public on Jul 08, 2020
Title BMDM_KO_0h_3
Sample type SRA
 
Source name femurs and tibias
Organism Mus musculus
Characteristics time: 0h
strain: C57BL/6
cell type: bone marrow-derived macrophage
genotype: lncFAO knockout
gender: male
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 NEBNext Poly(A) RNA Magneic Isolation Module (NEB), after which RNA-seq libraries were prepared using a NEBNext Ultra II 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
 
Data processing Reads were aligned to the mm10 mouse genome using STAR.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph files were generated using Homer.
 
Submission date Apr 04, 2020
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 GPL18480
Series (1)
GSE129961 Analysis of lncRNAs in macrophages
Relations
BioSample SAMN14538795
SRA SRX8059207

Supplementary file Size Download File type/resource
GSM4453906_BMDM_KO_0h_3.ucsc.bedGraph.gz 85.7 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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