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Status |
Public on Dec 21, 2022 |
Title |
BMDM_PRX_LPS8h_rep1 |
Sample type |
SRA |
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Source name |
Bone marrow-derived macrophage
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Organism |
Mus musculus |
Characteristics |
strain: C57BL/6
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Treatment protocol |
For LPS treatment, 100 ng/ml of LPS (Sigma-Aldrich) was added to the medium.
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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.
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 1500 |
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Description |
PRX-treated, LPS-treated
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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.
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Submission date |
Mar 02, 2020 |
Last update date |
Dec 21, 2022 |
Contact name |
Ichiro Manabe |
E-mail(s) |
manabe-tky@umin.ac.jp
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Organization name |
Chiba University
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Street address |
1-8-1 Inohana, Chuo
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City |
Chiba |
ZIP/Postal code |
260-8670 |
Country |
Japan |
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Platform ID |
GPL18480 |
Series (1) |
GSE146236 |
Analysis of effects of polyrotaxane on macrophages |
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Relations |
BioSample |
SAMN14259009 |
SRA |
SRX7827888 |
Supplementary file |
Size |
Download |
File type/resource |
GSM4368662_BMDM_PRX_LPS8h_rep1.bedGraph.gz |
24.9 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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