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| Status |
Public on Jul 08, 2020 |
| Title |
BMDM_WT_24h_3 |
| Sample type |
SRA |
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| Source name |
femurs and tibias
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| Organism |
Mus musculus |
| Characteristics |
time: 24h
strain: C57BL/6
cell type: bone marrow-derived macrophage
genotype: wild-type
gender: male
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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 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.
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
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| 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.
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| Submission date |
Apr 04, 2020 |
| Last update date |
Jul 08, 2020 |
| 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) |
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| Relations |
| BioSample |
SAMN14538798 |
| SRA |
SRX8059234 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4453933_BMDM_WT_24h_3.ucsc.bedGraph.gz |
72.7 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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